Attenuated influenza viruses and vaccines

ABSTRACT

This invention provides highly attenuated influenza viruses and vaccines. The attenuated viruses and vaccines proliferate well and have high safety factors. The attenuated viruses providing protective immunity from challenge by virus of the same subtype, as well as cross protection against heterologous viruses.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 14/777,204, filed Sep. 15, 2015, which is a 371 of PCT/US2014/030027, filed Mar. 15, 2014, which claims the benefit of priority to U.S. Application No. 61/794,617, filed Mar. 15, 2013, all of which are incorporated herein by reference in their entireties.

FEDERAL FUNDING

This invention was made with government support under AI015122 and AI075219 awarded the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

This invention provides highly attenuated influenza viruses and vaccines. The attenuated viruses and vaccines proliferate well and have high safety factors. The attenuated viruses providing protective immunity from challenge by virus of the same subtype, as well as cross protection against heterologous viruses.

BACKGROUND OF THE INVENTION

Influenza is a human disease that leads every year to >30,000 deaths in the US and several hundred thousand deaths globally (1). Major neutralization antigenic proteins, hemagglutinin (HA) and neuraminidase (NA) on the virion surface, provide protecting immunity, but undergo yearly genetic variation by point mutations (genetic drift). This renders the viruses resistant to population immunity and set the stage for seasonal epidemics. Further, influenza virus may acquire a new antigenic make-up (reassortment of heterologous genes, referred to as genetic shift) leading to pandemics. Because the flu is seasonal and variable, new vaccines must be produced every year. This is made more complex since more than one type or strain of influenza virus co-circulates in any flu season, a phenomenon demanding that more than one new vaccine may have to be developed every year.

Currently, only two major types of vaccines are licensed, the intramuscularly administered inactivated vaccines (“Flu shot”), and the live attenuated vaccine (LAIV), given intra-nasally (“FluMist®”). The efficacy of the two vaccines is suboptimal. The injectable inactivated vaccines that requires a large quantity of starting material (the equivalent of approximately 10¹⁰ plaque-forming units, PFU, per dose), are incapable of inducing significant cell-mediated immunity, which is being recognized as an important determinant of protection (4). Moreover, the overall efficacy of the inactivated vaccine in the U.S. adult population aged 18-65 years is only 59% (5). The LAIV “FluMist,” on the other hand, induces both humoral and cellular immunity but it is restricted in use to people 2 to 49 yr of age (6, 7). Moreover, recurrent administration of LAIV, which always uses the same attenuating viral backbone, could result in tolerance in repeat recipients (8).

Influenza viruses that have been classified as type A, B, and C, are enveloped, negative-strand RNA viruses of Orthomyxoviridae of which subtypes of type A are the major culprit of human disease (3). The viruses transcribe and replicate their multipartite genome in the cell nucleus, each segment encoding one or two polypeptides. Of these the most important antigenic molecules are the glycoproteins hemagglutinin (HA) and neuraminidase (NA).

SUMMARY OF THE INVENTION

A long-held dogma posits that strong presentation to the immune system of the dominant influenza virus glycoprotein antigens hemagglutinin (HA) and neuraminidase (NA) is paramount for inducing protective immunity against influenza virus infection. It has now been discovered that attenuated viruses in which expression of the two dominant influenza virus glycoprotein antigens, HA and NA, is reduced, are highly effective in providing long lasting protective immunity against lethal wild type challenge and cross protection against diverse subtypes. Further, the viruses have exceptional safety profiles. Accordingly, the invention provides an attenuated influenza virus in which expression of hemagglutinin (HA) and neuraminidase (NA) is reduced. In certain embodiments, HA and NA are the only the only virus proteins having reduced expression. In other embodiments of the invention, the expression of one or more other virus proteins may also be reduced, such as, for example, PA, PB1, PB2, NP, NS, Ml, or M2. In certain embodiments, when the expression of a virus proteins other than HA and NA is reduced, the reduction is small compared to the reduction of HA and NA. According to the invention, reduction in expression of virus proteins of the invention is accomplished by changes in protein encoding sequence, for example by lowering the codon pair bias of the protein-encoding sequence, substituting rare codons, modifying G+C content, modifying CG and/or TA (or UA) dinucleotide content, or combinations. Reduced expression can also be accomplished by modifications to the regulatory sequences of the proteins.

In one such embodiment, reducing the codon-pair bias comprises identifying a codon pair in the parent protein-encoding sequence having a codon-pair score that can be reduced, and reducing the codon-pair bias by substituting the codon pair with a codon pair that has a lower codon-pair score. In another such embodiment, reducing the codon-pair bias comprises rearranging the codons of a parent protein-encoding sequence. In certain embodiments, the reduced-expression HA protein-encoding sequence and the reduced-expression NA protein-encoding sequence individually have a codon pair bias less than −0.1, or less than −0.2, or less than −0.3, or less than −0.4. Codon pair bias of a protein-encoding sequence (i.e., an open reading frame) is calculated as described in Coleman et al., 2000 (ref 12) and herein.

In an embodiment of the invention, expression of one or both of the HA protein-encoding sequence and the NA protein-encoding sequence is reduced by replacing one or more codons with synonymous codons that are less frequent in the host.

The invention further provides an influenza vaccine composition for inducing a protective immune response in a subject, wherein the vaccine composition comprises virus in which expression of HA is reduced and expression of NA is reduced. In certain embodiments, only expression of HA and NA is reduced. In some embodiments, expression of another virus protein is also reduced.

The invention also provides a method of eliciting a protective immune response in a subject comprising administering to the subject a prophylactically or therapeutically effective dose of a vaccine composition comprising an attenuated influenza virus, wherein expression of HA is reduced and expression of NA is reduced. In certain embodiments, only expression of HA and NA is reduced. In some embodiments, expression of another virus protein is also reduced. In an embodiment of the invention, an immune response is elicited that is effective against influenza of the same subtype as the attenuated virus of the vaccine. In another embodiment, an immune response is elicited that is effective against a heterologous influenza virus.

The invention also provides a method of making an attenuated influenza virus genome comprising a) obtaining the nucleotide sequence encoding the hemagglutinin protein of an influenza virus and the nucleotide sequence encoding the neuraminidase protein of an influenza virus, b) recoding the hemagglutinin-encoding nucleotide sequence to reduce expression and recoding the neuraminidase-encoding nucleotide sequence to reduce expression, and substituting the recoded nucleotide sequences into an influenza virus genome to make an attenuated influenza virus genome. In certain embodiments, only expression of HA and NA is reduced. In some embodiments, expression of another virus protein is also reduced.

DESCRIPTION OF THE FIGURES

FIGS. 1A-1D. Construction of variants having reduced codon pair bias and phenotypes in tissue cultures. (FIG. 1A) NA^(Min) and HA^(Min) were designed (leaving 120-200 nt long wt sequences at 5′ and 3′ ends) and constructed by chemical synthesis. They were then used to replace by reverse genetics (13) one or two corresponding genes of wt PR8. The number of synonymous mutations is shown. (FIG. 1B) Recovered viruses were analyzed for plaque size phenotypes on MDCK monolayers. (FIG. 1C) Growth kinetics of wt PR8 and reduced codon-pair bias variants were analyzed on MDCK cells after infections at an MOI of 0.01. Every three hours post-infection, cell supernatants were collected and analyzed for virus titers by plaque assays. (FIG. 1D) Growth kinetics of wt PR8 and (NA+HA)^(Min) virus in A549 cells. Cells were infected at an MOI of 1.

FIGS. 2A-2B. Protein expression and mRNA levels in (NA+HA)^(Min)-infected in tissue culture cells. MDCK cells were infected with (NA+HA)^(Min) or wt PR8 at a MOI of 5. (FIG. 2A) Western blot analyses were performed to determine the viral protein expression the infected cells at 3 h and 6 h p.i. (FIG. 2B) Northern blot analyses were performed to determine mRNA levels of HA, NA, PB1 and GAPDH in (NA+HA)^(Min) or wt PR8-infected MDCK cells. At 3, 6, and 9 h p.i., cytoplasmic mRNA were collected and analyzed. For HA^(Min) and HA^(WT) transcript probes, the same 150 nt that recognized the common 3′ end of the respective genes was used. Similarly, the probes for NA^(Min) and NA^(WT) have the same 150 nt sequence corresponding to the common 3′ end of the NA genes.

FIGS. 3A-3F. Virus phenotypes in infected mice. (FIGS. 3A and 3B) Measurement of the median lethal dose (LD₅₀). Groups of five male Balb/C mice were intranasally infected with the (NA+HA)^(Min) variant at 10⁴, 10⁵, or 10⁶ PFU and the relative body weight and survival rate were monitored for 14 days p.i. Mice that lost 25% of their body weight were euthanized. LD₅₀ was calculated based on the method of Reed-Muench (24). (FIGS. 3C and 3D) Measurement of the median protective dose (PD₅₀). Groups of five male Balb/C mice were vaccinated with 10², 10¹, or 10⁰ PFU of (NA+HA)^(Min) on day 0. On day 28 post vaccination, all mice were challenged with 10⁵ PFU wt PR8 virus. The relative body weight and survival rate after challenge were monitored. PD₅₀ was calculated based on the method of Reed-Muench (24). (FIGS. 3E and 3F) Safe and effective vaccine range of the (NA+HA)^(Min) (open box) and wt PR8 virus (gray zone) were plotted. Any vaccine dose within this region warranted survival of the animals, and also completely protected them from lethal homogeneous challenge. Error bars represent SD.

FIGS. 4A-4B. Virus titers in lungs of infected mice. (FIG. 4A) Groups of three male Balb/C mice were infected with 10⁴ PFU of wt PR8 or (NA+HA)^(Min). On day 1, 3, 5, 7, 9 and 11 p.i., the mice were euthanized and their lungs harvested and homogenized. Viral titers in the homogenates were determined by plaque assays on MDCK cells. * All wt PR8-infected mice were dead on day 5. ‡ The virus titers in (NA+HA)^(Min)-infected mice after day 9 were undetectable (less than 4 PFU). (FIG. 4B) Comparison of virus titers in lungs of three mice each infected with wt PR8 or (NA+HA)^(Min) at a dose from 10¹ to 10⁴ PFU. The lungs of the animals were harvest on day 3, and plaque assays were performed to determine virus titers. Error bars represent SD.

FIGS. 5A-5D. Cross protection against H3N2 virus infections in (NA+HA)^(Min)(H1N1)-vaccinated mice. Groups of five Balb/c mice were vaccinated with (NA+HA)^(Min) at different doses. On day 28 post vaccination, mice were challenged with (FIGS. 5A and 5B) 100 LD₅₀ heterologous viruses A/Aichi/2/1968 (H3N2) virus (=1.5×10⁴ PFU). Survival rate and relative body weights were monitored for 14 days. All mice vaccinated with at least 10³ PFU of (NA+HA)^(Min)(H1N1) survived the lethal challenge. The cross protection PD₅₀ against H3N2 Aichi virus calculated is 237 PFU. (FIGS. 5C and 5D) Mice vaccinated with (NA+HA)^(Min) virus were also challenged with 100 LD₅₀ A/Victoria/3/75 (H3N2) virus (=3.2×104 PFU). Survival rate and relative body weights were monitored for 14 days. All mice vaccinated with at least 10³ PFU of (NA+HA)^(Min)(H1N1) survived the lethal challenge. The cross protection PD₅₀ against H3N2 Victoria virus calculated is 147 PFU based on the method of Reed-Muench (24). Error bars represent SD.

FIG. 6. Hemagglutination inhibition (HAI) assay with serum of vaccinated mice. Mice were infected at different doses with PR8 or (NA+HA)^(Min). Serum was collected on day 28 p.i. and antibody titers were determined by hemagglutination inhibition assays, as described in Material and Methods. Mice were then challenged with 10⁵ PFU wt PR8 and survival rates were monitored. Gray labeled dots indicated mice that did not survive.

FIGS. 7A-7D. LD₅₀ and PD₅₀ values of NA^(Min) in mice. (FIGS. 7A and 7B) Groups of five male Balb/c mice were infected intranasally with different doses of NA^(Min) variant. The relative body weight and survival rate were monitored for 14 days. The LD₅₀ calculated was 2.4×10⁵ PFU. (C and D) Groups of five males were vaccinated with different dose of NA^(Min) variant, 28 days p.i., mice were challenged with 10⁵ PFU wt influenza A/PR/8/34 (PR8). The relative body weight and survival rate were monitored for 14 days. Error bars represent SD.

FIGS. 8A-8B. Long term protection of (NA+HA)^(Min)-vaccinated mice. Groups of five Balb/c mice (5-6 weeks) were infected intranasally with (NA+HA)^(Min) at different doses. After seven months, mice were challenged with 10⁵ PFU wt PR8. Their body weight and survival rate were monitored for 14 days. Error bars represent SD.

FIGS. 9A-9D. Composition of (NA+HA)^(Min) virus. WT and (NA+HA)^(Min) virus were purified by sucrose gradient. Equivalent amounts of PFUs were compared to determine the relative amounts of the indicated virus proteins. (FIG. 9A) Commassie stain. (FIGS. 9B and 9C) silver stain. (FIG. 9D) Western blot.

FIGS. 10A-10B. Expression of virus proteins and mRNAs in MDCK cells infected with WT influenza or (NA+HA)^(Min). (FIG. 10A) ³⁵S labeled proteins in infected MDCK cells. (FIG. 10B) Northern analysis of viral mRNAs expressed in infected MDCK.

FIG. 11. Passive immunization with Serum from PR8-(NA+HA)^(Min) vaccinated mice protects naïve mice from homologous WT PR8 challenge. FIG. 11 shows mice passively immunized with PR8-(NA+HA)^(Min) sera survived and remained healthy upon challenge with WT virus.

FIGS. 12A-12B. Passive immunization with serum from PR8-(NA+HA)^(Min) (H1N1) vaccinated mice protects naïve mice from heterologous challenge with an H3N2 virus. FIG. 11 shows mice passively immunized with PR8-(NA+HA)^(Min) sera maintained weight (Panel A) and had improved survival (Panel B) when challenged with H3N2 virus.

FIGS. 13A-13B. Assessment of cross protection against H3N2 viruses conferred by immunization with PR8-(NA+HA)^(Min). (FIG. 13A) Inhibition of hemagglutination by sera from PR8-(NA+HA)^(Min) immunized mice. (FIG. 13B) Neutralization of virus infection of MDCK cells by sera from PR8-(NA+HA)^(Min) immunized mice.

FIG. 14. Growth of WT and PR8-(NA+HA)^(Min) virus in MDCK cells and MDCK cells transfected to express α-2,6-sialyltransferase.

FIG. 15. T cell responses in lungs of Balb/C mice 7 days post-infection. Cell numbers are expressed as total cell count in lung (left panels) or percentage of CD45⁺ cells (right panels).

FIG. 16. B cell responses in lungs of Balb/C mice 7 days post-infection. Cell numbers are expressed as total cell count in lung (upper panel) or percentage of CD45⁺ cells (lower panels).

FIG. 17. T cell responses in spleens of Balb/C mice 7 days post-infection.

FIG. 18. T cell responses in spleens of Balb/C mice 7 days post-infection.

FIGS. 19A-19I. Immune cell infiltration of lung tissue 3 days post-infection. (FIG. 19A) CD45⁺ leukocytes, (FIG. 19B) CD45⁺ Ly6G^(high) polymorphonuclear leukocytes (PMN), (FIG. 19C) CD45⁺CD11c⁺ I-A^(d+) F4/80⁻ dendritic cells, (FIG. 19D) CD45⁺ NKp46+ natural killer cells, (FIG. 19E) CD45⁺CD11b⁺Ly6C^(high)Ly6G⁻ inflammatory monocytes, (FIG. 19F) CD45⁺ I-A^(d+) F4/80⁺ macrophages, (G) CD45⁺CD3⁺CD4⁺ T helper cells, (FIG. 19H) CD45⁺ CD19⁺ B cells, and (FIG. 19I) CD45⁺CD19⁺IgM⁺ B cells.

DETAILED DESCRIPTION

The present invention relates to the production of attenuated influenza viruses that can be used to protect against viral infection and disease. A basic premise in flu vaccination is adequate delivery of HA and NA to vaccine recipients assuming that a very high dose (“Flu shot”) or a dose corresponding to live viral infection (“FluMist”) of these traditionally dominant antigenic polypeptides alone are sufficient for adequate vaccine efficacy. Those expectations aside, the present invention benefits from a contrary approach. The invention provides attenuated influenza viruses in which expression of HA and NA is reduced, which have excellent growth properties useful to vaccine production, yet possess an extraordinary safety profile and enhanced protective characteristics. The attenuated viruses proliferate nearly as well as wild type virus, have highly attenuated phenotypes, as revealed by LD₅₀ values, are unusually effective in providing protective immunity against challenge by influenza virus of the same subtype, and also provide protective immunity against challenge by influenza virus of other subtypes.

In certain attenuated viruses of the invention, the expression of one or more other virus proteins may also be reduced, such as, for example, PA, PB1, PB2, NP, NS, M1, or M2. In certain embodiments, when the expression of a virus proteins other than HA and NA is reduced, the reduction is small compared to the reduction of HA and NA.

In certain attenuated influenza viruses of the invention, expression of hemagglutinin (HA) and neuraminidase (NA) is reduced, and expression of other influenza proteins (i.e., NP, M (including M1 and M2), NS, PA, PB1, and PB2 protein is not substantially changed (i.e., substantially reduced or increased). In an embodiment of the invention, expression of NP, PA, PB1, and PB2 is not substantially reduced. That expression of the NP, M (including M1 and M2), NS, PA, PB1, and PB2 protein encoding sequences is not substantially reduced means that in embodiments where there is a small change in expression of one or more of those proteins (e.g., NP, PA, PB1, PB2, M, and or M), the change in expression of those proteins has little or no effect on attenuation. Little or no effect on attenuation includes one or both of the following: 1) Any reduced expression of NP, M (including M1 and M2), NS, PA, PB1, or PB2 does not reduce viral replication or viral infectivity more than 20% when the NP, M (including M1 and M2), NS, PA, PB1, or PB2 is expressed at the reduced level in a test influenza virus in which only the level of that protein is reduced; 2) The level of expression of NP, M (including M1 and M2), NS, PA, PB1, or PB2 is reduced by less than 20% in the attenuated virus in which expression of HA and NA is reduced.

In certain embodiments of the invention, the attenuated influenza viruses of the invention comprise a recoded hemagglutinin (HA) nucleic acid and a recoded neuraminidase (NA) nucleic acid. In certain of these embodiments, another virus protein, such as NP, M (including M1 and M2), NS, PA, PB1, or PB2 , is recoded. In others of these embodiments, other protein encoding sequences (i.e., NP, M (including M1 and M2), NS, PA, PB1, and PB2 protein encoding sequences are not recoded. That the NP, M (including M1 and M2), NS, PA, PB1, and PB2 protein encoding sequences are not recoded does not exclude mutations and other variations in those sequences, but only means that any mutations or variations made in those sequences have little or no effect on attenuation. Little or no effect on attenuation includes one or both of the following: 1) The mutations or variations in the NP, M (including M1 and M2), NS, PA, PB1, or PB2 sequence do not reduce viral replication or viral infectivity more than 20% when the variant NP, M (including M1 and M2), NS, PA, PB1, or PB2 nucleic acid sequence is the only variant in a test influenza virus; 2) Mutations or variations in any of the NP, M (including M1 and M2), NS, PA, PB1, or PB2 nucleic acid represent fewer than 10% of the nucleotides in that coding sequence.

The viruses of the invention are highly attenuated. In embodiments of the invention, compared to wild type, the viruses are at least 5,000 fold attenuated, or at least 10,000 fold attenuated, or at least 20,000 fold attenuated, or at least 33,000 fold attenuated, or at least 50,000 fold attenuated, of at least 100,000 fold attenuated in the BALB/c mouse model compared to a wild type virus having proteins of the same sequence but encoded by a different nucleotide sequence.

The attenuated viruses are also highly protective against wild type virus of the same subtype. In embodiments of the invention, the protective dose (PD₅₀) of the viruses is less than 100 PFU, or less than 50 PFU, or less than 20 PFU, or less than 10 PFU, or less than 5 PFU, when measured by a mouse model, such as exemplified herein.

The attenuated viruses of the invention also exhibit a large margin of safety (i.e., the difference between LD₅₀ and PD₅₀), thus have high safety factors, defined herein as the ratio of LD₅₀/PD₅₀. In certain embodiments of the invention, the safety factor is at least 10², or at least 10³, or at least 10⁴, or at least 10⁵, or at least 2×10⁵, or at least 5×10⁵, or at least 10⁶, or at least 2×10⁶, or at least 5×10⁶. In certain embodiments, the safety factor is from 10² to 10³, or from 10³ to 10⁴, or from 10⁴ to 10⁵, or from 10⁵ to 10⁶.

The attenuated viruses of the invention are also highly protective against heterologous viruses. In certain embodiments of the invention, the protective dose (PD₅₀) of an attenuated virus of the invention is less than 1000 PFU, or less than 500 PFU, or less than 200 PFU, or less than 100 PFU, when measured by a mouse model, such as exemplified herein

The recoding of HA and NA protein encoding sequences of the attenuated viruses of the invention can have been made utilizing any algorithm or procedure known in the art or newly devised for recoding a protein encoding sequence. According to the invention, nucleotide substitutions are engineered in multiple locations in the HA and NA coding sequences, wherein the substitutions introduce a plurality of synonymous codons into the genome. In certain embodiments, the synonymous codon substitutions alter codon bias, codon pair bias, the density of infrequent codons or infrequently occurring codon pairs, RNA secondary structure, CG and/or TA (or UA) dinucleotide content, C+G content, translation frameshift sites, translation pause sites, the presence or absence microRNA recognition sequences or any combination thereof, in the genome. The codon substitutions may be engineered in multiple locations distributed throughout the HA and NA coding sequences, or in the multiple locations restricted to a portion of the HA and NA coding sequences. Because of the large number of defects (i.e., nucleotide substitutions) involved, the invention provides a means of producing stably attenuated viruses and live vaccines.

As discussed further below, in some embodiments, a virus coding sequence is recoded by substituting one or more codon with synonymous codons used less frequently in the influenza host (e.g., humans, birds, pigs). In some embodiments, a virus coding sequence is recoded by substituting one or more codons with synonymous codons used less frequently in the influenza virus. In certain embodiments, the number of codons substituted with synonymous codons is at least 5. In some embodiments, at least 10, or at least 20 codons are substituted with synonymous codons.

In some embodiments, virus codon pairs are recoded to reduce (i.e., lower the value of) codon-pair bias. In certain embodiments, codon-pair bias is reduced by identifying a codon pair in an HA or NA coding sequence having a codon-pair score that can be reduced and reducing the codon-pair bias by substituting the codon pair with a codon pair that has a lower codon-pair score. In some embodiments, this substitution of codon pairs takes the form of rearranging existing codons of a sequence. In some such embodiments, a subset of codon pairs is substituted by rearranging a subset of synonymous codons. In other embodiments, codon pairs are substituted by maximizing the number of rearranged synonymous codons. It is noted that while rearrangement of codons leads to codon-pair bias that is reduced (made more negative) for the virus coding sequence overall, and the rearrangement results in a decreased CPS at many locations, there may accompanying CPS increases at other locations, but on average, the codon pair scores, and thus the CPB of the modified sequence, is reduced. In some embodiments, recoding of codons or codon-pairs can take into account altering the G+C content of the HA and NA coding sequences. In some embodiments, recoding of codons or codon-pairs can take into account altering the frequency of CG and/or TA dinucleotides in the HA and NA coding sequences.

In certain embodiments, the recoded (i.e., reduced-expression) HA protein-encoding sequence has a codon pair bias less than −0.1, or less than −0.2, or less than −0.3, or less than −0.4. In certain embodiments, the recoded (i.e., reduced-expression) NA protein-encoding sequence has a codon pair bias less than −0.1, or less than −0.2, or less than −0.3, or less than −0.4. In certain embodiments, the codon pair bias of the recoded HA protein encoding sequence is reduced by at least 0.1, or at least 0.2, or at least 0.3, or at least 0.4, compared to the parent HA protein encoding sequence from which it is derived. In certain embodiments, the codon pair bias of the recoded NA protein encoding sequence is reduced by at least 0.1, or at least 0.2, or at least 0.3, or at least 0.4, compared to the parent NA protein encoding sequence from which it is derived. In certain embodiments, rearrangement of synonymous codons of the HA protein-encoding sequence provides a codon-pair bias reduction of at least 0.1, or at least 0.2, or at least 0.3, or at least 0.4, parent HA protein encoding sequence from which it is derived. In certain embodiments, rearrangement of synonymous codons of the NA protein-encoding sequence provides a codon-pair bias reduction of at least 0.1, or at least 0.2, or at least 0.3, or at least 0.4, parent NA protein encoding sequence from which it is derived.

Usually, these substitutions and alterations are made and reduce expression of the encoded virus proteins without altering the amino acid sequence of the encoded protein. In certain embodiments, the invention also includes alterations in the HA and/or NA coding sequences that result in substitution of non-synonymous codons an amino acid substitutions in the encoded protein, which may or may not be conservative.

Most amino acids are encoded by more than one codon. See the genetic code in Table 1. For instance, alanine is encoded by GCU, GCC, GCA, and GCG. Three amino acids (Leu, Ser, and Arg) are encoded by six different codons, while only Trp and Met have unique codons. “Synonymous” codons are codons that encode the same amino acid. Thus, for example, CUU, CUC, CUA, CUG, UUA, and UUG are synonymous codons that code for Leu. Synonymous codons are not used with equal frequency. In general, the most frequently used codons in a particular organism are those for which the cognate tRNA is abundant, and the use of these codons enhances the rate and/or accuracy of protein translation. Conversely, tRNAs for the rarely used codons are found at relatively low levels, and the use of rare codons is thought to reduce translation rate and/or accuracy.

TABLE 1 Genetic Code^(a) U C A G U Phe Ser Tyr Cys U Phe Ser Tyr Cys C Leu Ser STOP STOP A Leu Ser STOP Trp G C Leu Pro His Arg U Leu Pro His Arg C Leu Pro Gln Arg A Leu Pro Gln Arg G A Ile Thr Asn Ser U Ile Thr Asn Ser C Ile Thr Lys Arg A Met Thr Lys Arg G G Val Ala Asp Gly U Val Ala Asp Gly C Val Ala Glu Gly A Val Ala Glu Gly G ^(a)The first nucleotide in each codon encoding a particular amino acid is shown in the left-most column; the second nucleotide is shown in the top row; and the third nucleotide is shown in the right-most column.

Codon Bias

As used herein, a “rare” codon is one of at least two synonymous codons encoding a particular amino acid that is present in an mRNA at a significantly lower frequency than the most frequently used codon for that amino acid. Thus, the rare codon may be present at about a 2-fold lower frequency than the most frequently used codon. Preferably, the rare codon is present at least a 3-fold, more preferably at least a 5-fold, lower frequency than the most frequently used codon for the amino acid. Conversely, a “frequent” codon is one of at least two synonymous codons encoding a particular amino acid that is present in an mRNA at a significantly higher frequency than the least frequently used codon for that amino acid. The frequent codon may be present at about a 2-fold, preferably at least a 3-fold, more preferably at least a 5-fold, higher frequency than the least frequently used codon for the amino acid. For example, human genes use the leucine codon CTG 40% of the time, but use the synonymous CTA only 7% of the time (see Table 2). Thus, CTG is a frequent codon, whereas CTA is a rare codon. Roughly consistent with these frequencies of usage, there are 6 copies in the genome for the gene for the tRNA recognizing CTG, whereas there are only 2 copies of the gene for the tRNA recognizing CTA. Similarly, human genes use the frequent codons TCT and TCC for serine 18% and 22% of the time, respectively, but the rare codon TCG only 5% of the time. TCT and TCC are read, via wobble, by the same tRNA, which has 10 copies of its gene in the genome, while TCG is read by a tRNA with only 4 copies. It is well known that those mRNAs that are very actively translated are strongly biased to use only the most frequent codons. This includes genes for ribosomal proteins and glycolytic enzymes. On the other hand, mRNAs for relatively non-abundant proteins may use the rare codons.

TABLE 2 Codon usage in Homo sapiens (source: http://www.kazusa.or.jp/codon/) Amino Acid Codon Number /1000 Fraction Gly GGG 636457.00 16.45 0.25 Gly GGA 637120.00 16.47 0.25 Gly GGT 416131.00 10.76 0.16 Gly GGC 862557.00 22.29 0.34 Glu GAG 1532589.00 39.61 0.58 Glu GAA 1116000.00 28.84 0.42 Asp GAT 842504.00 21.78 0.46 Asp GAC 973377.00 25.16 0.54 Val GTG 1091853.00 28.22 0.46 Val GTA 273515.00 7.07 0.12 Val GTT 426252.00 11.02 0.18 Val GTC 562086.00 14.53 0.24 Ala GCG 286975.00 7.42 0.11 Ala GCA 614754.00 15.89 0.23 Ala GCT 715079.00 18.48 0.27 Ala GCC 1079491.00 27.90 0.40 Arg AGG 461676.00 11.93 0.21 Arg AGA 466435.00 12.06 0.21 Ser AGT 469641.00 12.14 0.15 Ser AGC 753597.00 19.48 0.24 Lys AAG 1236148.00 31.95 0.57 Lys AAA 940312.00 24.30 0.43 Asn AAT 653566.00 16.89 0.47 Asn AAC 739007.00 19.10 0.53 Met ATG 853648.00 22.06 1.00 Ile ATA 288118.00 7.45 0.17 Ile ATT 615699.00 15.91 0.36 Ile ATC 808306.00 20.89 0.47 Thr ACG 234532.00 6.06 0.11 Thr ACA 580580.00 15.01 0.28 Thr ACT 506277.00 13.09 0.25 Thr ACC 732313.00 18.93 0.36 Trp TGG 510256.00 13.19 1.00 End TGA 59528.00 1.54 0.47 Cys TGT 407020.00 10.52 0.45 Cys TGC 487907.00 12.61 0.55 End TAG 30104.00 0.78 0.24 End TAA 38222.00 0.99 0.30 Tyr TAT 470083.00 12.15 0.44 Tyr TAC 592163.00 15.30 0.56 Leu TTG 498920.00 12.89 0.13 Leu TTA 294684.00 7.62 0.08 Phe TTT 676381.00 17.48 0.46 Phe TTC 789374.00 20.40 0.54 Ser TCG 171428.00 4.43 0.05 Ser TCA 471469.00 12.19 0.15 Ser TCT 585967.00 15.14 0.19 Ser TCC 684663.00 17.70 0.22 Arg CGG 443753.00 11.47 0.20 Arg CGA 239573.00 6.19 0.11 Arg CGT 176691.00 4.57 0.08 Arg CGC 405748.00 10.49 0.18 Gln CAG 1323614.00 34.21 0.74 Gln CAA 473648.00 12.24 0.26 His CAT 419726.00 10.85 0.42 His CAC 583620.00 15.08 0.58 Leu CTG 1539118.00 39.78 0.40 Leu CTA 276799.00 7.15 0.07 Leu CTT 508151.00 13.13 0.13 Leu CTC 759527.00 19.63 0.20 Pro CCG 268884.00 6.95 0.11 Pro CCA 653281.00 16.88 0.28 Pro CCT 676401.00 17.48 0.29 Pro CCC 767793.00 19.84 0.32

The propensity for highly expressed genes to use frequent codons is called “codon bias.” A gene for a ribosomal protein might use only the 20 to 25 most frequent of the 61 codons, and have a high codon bias (a codon bias close to 1), while a poorly expressed gene might use all 61 codons, and have little or no codon bias (a codon bias close to 0). It is thought that the frequently used codons are codons where larger amounts of the cognate tRNA are expressed, and that use of these codons allows translation to proceed more rapidly, or more accurately, or both. The PV capsid protein, for example, is very actively translated, and has a high codon bias.

Codon Pair Bias

In addition, a given organism has a preference for the nearest codon neighbor of a given codon A, referred to a bias in codon pair utilization. A change of codon pair bias, without changing the existing codons, can influence the rate of protein synthesis and production of a protein.

Codon pair bias may be illustrated by considering the amino acid pair Ala-Glu, which can be encoded by 8 different codon pairs. If no factors other than the frequency of each individual codon (as shown in Table 2) are responsible for the frequency of the codon pair, the expected frequency of each of the 8 encodings can be calculated by multiplying the frequencies of the two relevant codons. For example, by this calculation the codon pair GCA-GAA would be expected to occur at a frequency of 0.097 out of all Ala-Glu coding pairs (0.23×0.42; based on the frequencies in Table 2). In order to relate the expected (hypothetical) frequency of each codon pair to the actually observed frequency in the human genome the Consensus CDS (CCDS) database of consistently annotated human coding regions, containing a total of 14,795 human genes, was used. This set of genes is the most comprehensive representation of human coding sequences. Using this set of genes the frequencies of codon usage were re-calculated by dividing the number of occurrences of a codon by the number of all synonymous codons coding for the same amino acid. As expected the frequencies correlated closely with previously published ones such as the ones given in Table 2. Slight frequency variations are possibly due to an oversampling effect in the data provided by the codon usage database at Kazusa DNA Research Institute (http://www.kazusa.or.jp/codon/codon.html) where 84949 human coding sequences were included in the calculation (far more than the actual number of human genes). The codon frequencies thus calculated were then used to calculate the expected codon-pair frequencies by first multiplying the frequencies of the two relevant codons with each other (see Table 3 expected frequency), and then multiplying this result with the observed frequency (in the entire CCDS data set) with which the amino acid pair encoded by the codon pair in question occurs. In the example of codon pair GCA-GAA, this second calculation gives an expected frequency of 0.098 (compared to 0.097 in the first calculation using the Kazusa dataset). Finally, the actual codon pair frequencies as observed in a set of 14,795 human genes was determined by counting the total number of occurrences of each codon pair in the set and dividing it by the number of all synonymous coding pairs in the set coding for the same amino acid pair (Table 3; observed frequency). Frequency and observed/expected values for the complete set of 3721 (61²) codon pairs, based on the set of 14,795 human genes, are provided herewith as Supplemental Table 1.

TABLE 3 Codon Pair Scores Exemplified by the Amino Acid Pair Ala-Glu amino acid codon expected observed obs/exp pair pair frequency frequency ratio AE GCAGAA 0.098 0.163 1.65 AE GCAGAG 0.132 0.198 1.51 AE GCCGAA 0.171 0.031 0.18 AE GCCGAG 0.229 0.142 0.62 AE GCGGAA 0.046 0.027 0.57 AE GCGGAG 0.062 0.089 1.44 AE GCTGAA 0.112 0.145 1.29 AE GCTGAG 0.150 0.206 1.37 Total 1.000 1.000

If the ratio of observed frequency/expected frequency of the codon pair is greater than one the codon pair is said to be overrepresented. If the ratio is smaller than one, it is said to be underrepresented. In the example the codon pair GCA-GAA is overrepresented 1.65 fold while the coding pair GCC-GAA is more than 5-fold underrepresented.

Many other codon pairs show very strong bias; some pairs are under-represented, while other pairs are over-represented. For instance, the codon pairs GCCGAA (AlaGlu) and GATCTG (AspLeu) are three- to six-fold under-represented (the preferred pairs being GCAGAG and GACCTG, respectively), while the codon pairs GCCAAG (AlaLys) and AATGAA (AsnGlu) are about two-fold over-represented. It is noteworthy that codon pair bias has nothing to do with the frequency of pairs of amino acids, nor with the frequency of individual codons. For instance, the under-represented pair GATCTG (AspLeu) happens to use the most frequent Leu codon, (CTG).

As discussed more fully below, codon pair bias takes into account the score for each codon pair in a coding sequence averaged over the entire length of the coding sequence. According to the invention, codon pair bias is determined by

${CPB} = {\sum\limits_{i = 1}^{k}{\frac{CPSi}{k - 1}.}}$

Accordingly, similar codon pair bias for a coding sequence can be obtained, for example, by minimized codon pair scores over a subsequence or moderately diminished codon pair scores over the full length of the coding sequence.

Calculation of Codon Pair Bias.

Every individual codon pair of the possible 3721 non-“STOP” containing codon pairs (e.g., GTT-GCT) carries an assigned “codon pair score,” or “CPS” that is specific for a given “training set” of genes. The CPS of a given codon pair is defined as the log ratio of the observed number of occurances over the number that would have been expected in this set of genes (in this example the human genome). Determining the actual number of occurrences of a particular codon pair (or in other words the likelyhood of a particular amino acid pair being encoded by a particular codon pair) is simply a matter of counting the actual number of occurances of a codon pair in a particular set of coding sequences. Determining the expected number, however, requires additional calculations. The expected number is calculated so as to be independent of both amino acid frequency and codon bias similarly to Gutman and Hatfield. That is, the expected frequency is calculated based on the relative proportion of the number of times an amino acid is encoded by a specific codon. A positive CPS value signifies that the given codon pair is statistically over-represented, and a negative CPS indicates the pair is statistically under-represented in the human genome.

To perform these calculations within the human context, the most recent Consensus CDS (CCDS) database of consistently annotated human coding regions, containing a total of 14,795 genes, was used. This data set provided codon and codon pair, and thus amino acid and amino-acid pair frequencies on a genomic scale.

The paradigm of Federov et al. (2002), was used to further enhanced the approach of Gutman and Hatfield (1989). This allowed calculation of the expected frequency of a given codon pair independent of codon frequency and non-random associations of neighboring codons encoding a particular amino acid pair.

${S\left( P_{ij} \right)} = {{\ln\left( \frac{N_{O}\left( P_{ij} \right)}{N_{E}\left( P_{ij} \right)} \right)} = {\ln\left( \frac{N_{O}\left( P_{ij} \right)}{{F\left( C_{i} \right)}{F\left( C_{j} \right)}{N_{O}\left( X_{ij} \right)}} \right)}}$

In the calculation, P_(ij) is a codon pair occurring with a frequency of N_(O)(P_(ij)) in its synonymous group. C_(i) and C_(j) are the two codons comprising P_(ij), occuring with frequencies F(C_(i)) and F(C_(j)) in their synonymous groups respectively. More explicitly, F(C_(i)) is the frequency that corresponding amino acid X_(i) is coded by codon C_(i) throughout all coding regions and F(C_(i))=N_(O)(C_(i))/N_(O)(X_(i)), where N_(O)(C_(i)) and N_(O)(X_(i)) are the observed number of occurrences of codon C_(i) and amino acid X_(i) respectively. F(C_(j)) is calculated accordingly. Further, N_(O)(X_(ij)) is the number of occurrences of amino acid pair X_(ij) throughout all coding regions. The codon pair bias score S(P_(ij)) of P_(ij) was calculated as the log-odds ratio of the observed frequency N_(o)(P_(ij)) over the expected number of occurrences of N_(e)(P_(ij)).

Using the formula above, it was then determined whether individual codon pairs in individual coding sequences are over- or under-represented when compared to the corresponding genomic N_(e)(P_(ij)) values that were calculated by using the entire human CCDS data set. This calculation resulted in positive S(P_(ij)) score values for over-represented and negative values for under-represented codon pairs in the human coding regions (FIG. 7).

The “combined” codon pair bias of an individual coding sequence was calculated by averaging all codon pair scores according to the following formula:

${S\left( P_{ij} \right)} = {\sum\limits_{l = 1}^{k}{\frac{{S({Pij})}l}{k - 1}.}}$

The codon pair bias of an entire coding region is thus calculated by adding all of the individual codon pair scores comprising the region and dividing this sum by the length of the coding sequence.

Calculation of Codon Pair Bias, Implementation of Algorithm to Alter Codon-Pair Bias.

An algorithm was developed to quantify codon pair bias. Every possible individual codon pair was given a “codon pair score”, or “CPS”. CPS is defined as the natural log of the ratio of the observed over the expected number of occurrences of each codon pair over all human coding regions, where humans represent the host species of the instant vaccine virus to be recoded.

${CPS} = {\ln\left( \frac{{F({AB})}o}{\frac{{F(A)} \times {F(B)}}{{F(X)} \times {F(Y)}} \times {F({XY})}} \right)}$

Although the calculation of the observed occurences of a particular codon pair is straightforward (the actual count within the gene set), the expected number of occurrences of a codon pair requires additional calculation. We calculate this expected number to be independent both of amino acid frequency and of codon bias, similar to Gutman and Hatfield. That is, the expected frequency is calculated based on the relative proportion of the number of times an amino acid is encoded by a specific codon. A positive CPS value signifies that the given codon pair is statistically over-represented, and a negative CPS indicates the pair is statistically under-represented in the human genome

Using these calculated CPSs, any coding region can then be rated as using over- or under-represented codon pairs by taking the average of the codon pair scores, thus giving a Codon Pair Bias (CPB) for the entire gene.

${CPB} = {\sum\limits_{i = 1}^{k}\frac{CPSi}{k - 1}}$

The CPB has been calculated for all annotated human genes using the equations shown and plotted (FIG. 4). Each point in the graph corresponds to the CPB of a single human gene. The peak of the distribution has a positive codon pair bias of 0.07, which is the mean score for all annotated human genes. Also there are very few genes with a negative codon pair bias. Equations established to define and calculate CPB were then used to manipulate this bias.

Algorithm for Reducing Codon-Pair Bias.

Recoding of protein-encoding sequences may be performed with or without the aid of a computer, using, for example, a gradient descent, or simulated annealing, or other minimization routine. An example of the procedure that rearranges codons present in a starting sequence can be represented by the following steps:

1) Obtain wildtype viral genome sequence.

2) Select protein coding sequences to target for attenuated design.

3) Lock down known or conjectured DNA segments with non-coding functions.

4) Select desired codon distribution for remaining amino acids in redesigned proteins.

5) Perform random shuffle of at least two synonymous unlocked codon positions and calculate codon-pair score.

6) Further reduce (or increase) codon-pair score optionally employing a simulated annealing procedure.

7) Inspect resulting design for excessive secondary structure and unwanted restriction site:

-   -   if yes—>go to step (5) or correct the design by replacing         problematic regions with wildtype sequences and go to step (8).     -   8. Synthesize DNA sequence corresponding to virus design.     -   9. Create viral construct and assess viral phenotype:

if too attenuated, prepare subclone construct and go to 9; if insufficiently attenuated, go to 2.

Attenuation of viruses by reducing codon pair bias is disclosed in WO 2008/121992 and WO 2011/044561, which are incorporated by reference.

Attenuated Influenza Viruses

According to the invention, viral attenuation is accomplished by reducing expression of HA and NA coding sequences. One way to reduce expression of the coding sequences is by a reduction in codon pair bias, but other methods can also be used, alone or in combination. While codon bias may be changed, adjusting codon pair bias is particularly advantageous. For example, attenuating a virus through codon bias generally requires elimination of common codons, and so the complexity of the nucleotide sequence is reduced. In contrast, codon pair bias reduction or minimization can be accomplished while maintaining far greater sequence diversity, and consequently greater control over nucleic acid secondary structure, annealing temperature, and other physical and biochemical properties.

Codon pair bias of a protein-encoding sequence (i.e., an open reading frame) is calculated as set forth above and described in Coleman et al., 2000 (ref. 12).

Viral attenuation and induction or protective immune responses can be confirmed in ways that are well known to one of ordinary skill in the art, including but not limited to, the methods and assays disclosed herein. Non-limiting examples include plaque assays, growth measurements, reduced lethality in test animals, and protection against subsequent infection with a wild type virus.

In preferred embodiments, the invention provides viruses that are highly attenuated, and induce immunity against a plurality of influenza types and/or subtypes. Such flu varieties include viruses bearing all possible HA-NA combinations. Currently, there are 16 recognized hemagglutinins and nine neuraminidases, each of which has mutational variants. Examples of type A subtypes include, but are not limited to, H10N7, H10N1, H10N2, H10N3, H10N4, H10N5, H10N6, H10N7, H10N8, H10N9, H11N1, H11N2, H11N3, H11N4, H11N6, H11N8, H11N9, H12N1, H12N2, H12N4, H12N5, H12N6, H12N8, H12N9, H13N2, H13N3, H13N6, H13N9, H14N5, H14N6, H15N2, H15N8, H15N9, H16N3, H1N1, H1N2, H1N3, H1N5, H1N6, H1N8, H1N9, H2N1, H2N2, H2N3, H2N4, H2N5, H2N6, H2N7, H2N8, H2N9, H3N1, H3N2, H3N3, H3N4, H3N5, H3N6, H3N8, H3N9, H4N1, H4N2, H4N3, H4N4, H4N5, H4N6, H4N7, H4N8, H4N9, H5N1, H5N2, H5N3, H5N4, H5N6, H5N7, H5N8, H5N9, H6N1, H6N2, H6N3, H6N4, H6N5, H6N6, H6N7, H6N8, H6N9, H7N1, H7N2, H7N3, H7N4, H7N5, H7N7, H7N8, H7N9, H8N2, H8N4, H8N5, H9N1, H9N2, H9N3, H9N4, H9N5, H9N6, H9N7, H9N8, H9N9. Some subtypes of interest include, but are not limited to, H1N1 (one variant of which caused Spanish flu in 1918, another of which is pandemic in 2009), H2N2 (a variant of which caused Asian Flu in 1957), H3N2 (a variant of which caused Hong Kong Flu in 1968, H5N1 (a current pandemic threat), H7N7 (which has unusual zoonotic potential), and H1N2 (endemic in humans and pigs). Examples of attenuated influenza protein coding sequences are provided below.

TABLE 4 Reduced-Expression Influenza A Virus Genes WT Coding Sequence Recoded Coding Sequence SEQ ID SEQ ID Recoded Gene NO: CDS CPB NO Codons CPB H10N7 (A/northern shoveler/California/HKWF392sm/2007)(Avian) HA 1 1-1683 0.018 2 1-561 −0.441 NA 3 1-1494 0.009 4 1-498 −0.449 H1N1 (A/New York/3568/2009)(Human) HA 5 1-1698 0.043 6 1-566 −0.410 NA 7 1-1407 0.005 8 1-469 −0.456 H1N2 (A/New York/211/2003)(Human) HA 9 1-1695 0.036 10 1-565 −0.421 NA 11 1-1407 0.034 12 1-469 −0.476 H2N2 (A/Albany/22/1957)(Human) HA 13 1-1686 0.040 14 1-562 −0.422 NA 15 1-1407 0.008 16 1-469 −0.453 H3N2 (A/New York/933/2006)(Human) HA 17 1-1698 0.027 18 1-566 −0.447 NA 19 1-1407 0.041 20 1-469 −0.463 H5N1 (A/Jiangsu/1/2007)(Human) HA 21 1-1701 0.017 22 1-567 −0.435 NA 23 1-1347 0.009 24 1-449 −0.407 H7N2 (A/chicken/NJ/294508-12/2004)(Avian) HA 25 1-1656 0.036 26 1-552 −0.377 NA 27 1-1359 0.013 28 1-453 −0.491 H7N3 (A/Canada/rv504/2004)(Human) HA 29 1-1701 0.029 30 1-567 −0.405 NA 31 1-1407 0.042 32 1-469 −0.413 H7N7 (A/Netherlands/219/03)(Human) HA 33 1-1707 0.008 34 1-569 −0.447 NA 35 1-1413 −0.009 36 1-471 −0.423 H9N2 (A/Hong Kong/1073/99)(Human) HA 37 1-1680 0.021 38 1-560 −0.440 NA 39 1-1401 0.020 40 1-467 −0.453

Vaccine Compositions

The present invention provides a vaccine composition for inducing a protective immune response in a subject comprising any of the attenuated viruses described herein and a pharmaceutically acceptable carrier.

It should be understood that an attenuated virus of the invention, where used to elicit a protective immune response in a subject or to prevent a subject from becoming afflicted with a virus-associated disease, is administered to the subject in the form of a composition additionally comprising a pharmaceutically acceptable carrier. Pharmaceutically acceptable carriers are well known to those skilled in the art and include, but are not limited to, one or more of 0.01-0.1M and preferably 0.05M phosphate buffer, phosphate-buffered saline (PBS), or 0.9% saline. Such carriers also include aqueous or non-aqueous solutions, suspensions, and emulsions. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, saline and buffered media. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's and fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers such as those based on Ringer's dextrose, and the like. Solid compositions may comprise nontoxic solid carriers such as, for example, glucose, sucrose, mannitol, sorbitol, lactose, starch, magnesium stearate, cellulose or cellulose derivatives, sodium carbonate and magnesium carbonate. For administration in an aerosol, such as for pulmonary and/or intranasal delivery, an agent or composition is preferably formulated with a nontoxic surfactant, for example, esters or partial esters of C6 to C22 fatty acids or natural glycerides, and a propellant. Additional carriers such as lecithin may be included to facilitate intranasal delivery. Pharmaceutically acceptable carriers can further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives and other additives, such as, for example, antimicrobials, antioxidants and chelating agents, which enhance the shelf life and/or effectiveness of the active ingredients. The instant compositions can, as is well known in the art, be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to a subject.

In various embodiments of the instant vaccine composition, the attenuated virus (i) does not substantially alter the synthesis and processing of viral proteins in an infected cell; (ii) produces similar amounts of virions per infected cell as wt virus; and/or (iii) exhibits substantially lower virion-specific infectivity than wt virus. In further embodiments, the attenuated virus induces a substantially similar immune response in a host animal as the corresponding wt virus.

This invention also provides a modified host cell line specially isolated or engineered to be permissive for an attenuated virus that is inviable in a wild type host cell. Since the attenuated virus cannot grow in normal (wild type) host cells, it is absolutely dependent on the specific helper cell line for growth. This provides a very high level of safety for the generation of virus for vaccine production. Various embodiments of the instant modified cell line permit the growth of an attenuated virus, wherein the genome of said cell line has been altered to increase the number of genes encoding rare tRNAs.

In addition, the present invention provides a method for eliciting a protective immune response in a subject comprising administering to the subject a prophylactically or therapeutically effective dose of any of the vaccine compositions described herein. This invention also provides a method for preventing a subject from becoming afflicted with a virus-associated disease comprising administering to the subject a prophylactically effective dose of any of the instant vaccine compositions. In embodiments of the above methods, the subject has been exposed to a pathogenic virus. “Exposed” to a pathogenic virus means contact with the virus such that infection could result.

The invention further provides a method for delaying the onset, or slowing the rate of progression, of a virus-associated disease in a virus-infected subject comprising administering to the subject a therapeutically effective dose of any of the instant vaccine compositions.

As used herein, “administering” means delivering using any of the various methods and delivery systems known to those skilled in the art. Administering can be performed, for example, intranasally, intraperitoneally, intracerebrally, intravenously, orally, transmucosally, subcutaneously, transdermally, intradermally, intramuscularly, topically, parenterally, via implant, intrathecally, intralymphatically, intralesionally, pericardially, or epidurally. An agent or composition may also be administered in an aerosol, such as for pulmonary and/or intranasal delivery. Administering may be performed, for example, once, a plurality of times, and/or over one or more extended periods.

Eliciting a protective immune response in a subject can be accomplished, for example, by administering a primary dose of a vaccine to a subject, followed after a suitable period of time by one or more subsequent administrations of the vaccine. A suitable period of time between administrations of the vaccine may readily be determined by one skilled in the art, and is usually on the order of several weeks to months. The present invention is not limited, however, to any particular method, route or frequency of administration.

A “subject” means any animal or artificially modified animal. Animals include, but are not limited to, humans, non-human primates, cows, horses, sheep, pigs, dogs, cats, rabbits, ferrets, rodents such as mice, rats and guinea pigs, and birds. Artificially modified animals include, but are not limited to, SCID mice with human immune systems, and CD155tg transgenic mice expressing the human poliovirus receptor CD155. In a preferred embodiment, the subject is a human. Preferred embodiments of birds are domesticated poultry species, including, but not limited to, chickens, turkeys, ducks, and geese.

A “prophylactically effective dose” is any amount of a vaccine that, when administered to a subject prone to viral infection or prone to affliction with a virus-associated disorder, induces in the subject an immune response that protects the subject from becoming infected by the virus or afflicted with the disorder. “Protecting” the subject means either reducing the likelihood of the subject's becoming infected with the virus, or lessening the likelihood of the disorder's onset in the subject, by at least two-fold, preferably at least ten-fold. For example, if a subject has a 1% chance of becoming infected with a virus, a two-fold reduction in the likelihood of the subject becoming infected with the virus would result in the subject having a 0.5% chance of becoming infected with the virus. Most preferably, a “prophylactically effective dose” induces in the subject an immune response that completely prevents the subject from becoming infected by the virus or prevents the onset of the disorder in the subject entirely.

As used herein, a “therapeutically effective dose” is any amount of a vaccine that, when administered to a subject afflicted with a disorder against which the vaccine is effective, induces in the subject an immune response that causes the subject to experience a reduction, remission or regression of the disorder and/or its symptoms. In preferred embodiments, recurrence of the disorder and/or its symptoms is prevented. In other preferred embodiments, the subject is cured of the disorder and/or its symptoms.

Certain embodiments of any of the instant immunization and therapeutic methods further comprise administering to the subject at least one adjuvant. An “adjuvant” shall mean any agent suitable for enhancing the immunogenicity of an antigen and boosting an immune response in a subject. Numerous adjuvants, including particulate adjuvants, suitable for use with both protein- and nucleic acid-based vaccines, and methods of combining adjuvants with antigens, are well known to those skilled in the art. Suitable adjuvants for nucleic acid based vaccines include, but are not limited to, Quil A, imiquimod, resiquimod, and interleukin-12 delivered in purified protein or nucleic acid form. Adjuvants suitable for use with protein immunization include, but are not limited to, alum, Freund's incomplete adjuvant (FIA), saponin, Quil A, and QS-21.

The invention also provides a kit for immunization of a subject with an attenuated virus of the invention. The kit comprises the attenuated virus, a pharmaceutically acceptable carrier, an applicator, and an instructional material for the use thereof. In further embodiments, the attenuated virus may be one or more poliovirus, one or more rhinovirus, one or more influenza virus, etc. More than one virus may be preferred where it is desirable to immunize a host against a number of different isolates of a particular virus. The invention includes other embodiments of kits that are known to those skilled in the art. The instructions can provide any information that is useful for directing the administration of the attenuated viruses.

Throughout this application, various publications, reference texts, textbooks, technical manuals, patents, and patent applications have been referred to. The teachings and disclosures of these publications, patents, patent applications and other documents in their entireties are hereby incorporated by reference into this application to more fully describe the state of the art to which the present invention pertains. However, the citation of a reference herein should not be construed as an acknowledgement that such reference is prior art to the present invention.

It is to be understood and expected that variations in the principles of invention herein disclosed can be made by one skilled in the art and it is intended that such modifications are to be included within the scope of the present invention. The following Examples further illustrate the invention, but should not be construed to limit the scope of the invention in any way. Detailed descriptions of conventional methods, such as those employed in the construction of recombinant plasmids, transfection of host cells with viral constructs, polymerase chain reaction (PCR), and immunological techniques can be obtained from numerous publications, including Sambrook et al. (1989) and Coligan et al. (1994). All references mentioned herein are incorporated in their entirety by reference into this application. The contents of WO 2008/121992 and WO 2011/044561 are incorporated by reference.

EXAMPLES Example 1 Construction and Characterization of an HA and NA Codon Pair-Bias Reduced Influenza Virus in Tissue Culture

To achieve attenuation of influenza virus PR8, codon pair bias was reduced (introducing underrepresented codon pairs) in viral genes HA and NA according to computer algorithms (12, 13) and chemical synthesis (14), in order to reduce the expression level of the targeted viral genes.

Cells and viruses. MDCK, A549 and HEK293 T cell lines were maintained in DMEM supplemented with 10% FBS at 37° C. Influenza A/PR/8/34 (PR8) was cultured in MDCK cells.

Variant (NA+HA)^(Min) (618/3188 nt changes), combining the HA^(Min) (SEQ ID NO:53) and NA^(Min) (SEQ ID NO:60) genes, expressed growth and plaque phenotypes in MDCK cells comparable to those of the individual HA^(Min) and NA^(Min) variants (FIG. 1B, C). Similarly, a variant with a codon-pair bias reduced NA gene (NA^(Min), 265/1413 synonymous mutations; FIG. 1A) also replicated well in MDCK cells (FIG. 1C) and expressed an only slightly smaller plaque size phenotype (FIG. 1B) than wt PR8. In A549 cells the (NA+HA)^(Min) variant was highly attenuated (FIG. 1D), growing to a final titer three to four orders of magnitudes lower than wt PR8. A549 cells retain a complex signaling network that is related to the innate host response (15, 16).

Example 2 Levels of NA mRNA and HA Protein are Reduced in (NA+HA)^(Min)-Infected Cells

The apparent yield of HA polypeptide was examined by western blotting in MDCK cells at 3 h and 6 h post infection (p.i.) with 5 MOI of wt virus or (NA+HA)^(Min). Remarkably, at 6 h p.i., expression of HA protein was significantly reduced in (NA+HA)^(Min)-infected cells when compared to PR8-infected cells whereas PB1 and NS1 were synthesized to equal levels by viruses (FIG. 2A). Using the levels of PB1 and GAPDH mRNAs as control, the Northern blot analysis of mRNA levels in (NA+HA)^(Min)-infected cells indicated only a slight reduction of HA^(Min) mRNA at 3 h and 6 h (FIG. 2B).

In contrast, Northern blot analyses indicated an extensive reduction of the recoded NA^(Min) mRNA after 6 h and particularly after 9 h p.i. (FIG. 2B). Early in infection (3 h), the level of NA^(Min) mRNA was slightly reduced.

Example 3 Characterization of the Reduced Codon-Pair Bias Variants as Vaccine Candidates in Mice

The growth phenotype and pathogenesis of the (NA+HA)^(Min) variant was examined in an animal model. Groups of five BALB/c mice received (NA+HA)^(Min) at doses of 10⁴, 10⁵ or 10⁶ PFU intra-nasally, and body weight and survival of the animals was monitored continuously for 14 days p.i. (FIG. 3A, B). Morbidity and mortality (weight loss, reduced activity, death) was monitored. The Lethal Dose 50 (LD₅₀) of the wildtype virus and the vaccine candidates was calculated by the method of Reed and Muench (Reed, L. J.; Muench, H., 1938, The American Journal of Hygiene 27: 493-497). Remarkably, the (NA+HA)^(Min) variant did not induce apparent disease after a dose up to 10⁵ PFU. Even at 10⁶ PFU, mice only suffered transient weight loss, but all animals survived. Therefore, the theoretical LD₅₀ of the (NA+HA)^(Min) variant was calculated to be equal or greater than 3.16×10⁶ PFU, which exceeds that of wt PR8 by a factor of at least 100,000 (Table 1).

Whereas the (NA+HA)^(Min), HA^(Min), and NA^(Min) variants replicated with nearly equal efficiency and similar kinetics as wt PR8 in MDCK cells (FIG. 1C), the LD₅₀ of the variants were by orders of magnitude different: PR8=32 PFU, HA^(Min)=1.7×10³PFU (13), NA^(Min)=2.4×10⁵ PFU (FIG. 7, Table 5), and (NA+HA)^(Min)>3.3×10⁶. By itself, the NA^(Min) gene is about 100-fold more attenuated than the HA^(Min) gene, but reducing expression of NA and NP in the same virus significantly increases attenuation of the virus.

TABLE 5 LD₅₀ and PD₅₀ of Attenuated Virus LD₅₀ PD₅₀ WT PR8 3.2 × 10¹ ~1 NA^(Min) 2.4 × 10⁵ <32 HA^(Min) 1.7 × 10³ n.d. (NA + HA)^(Min) >3.3 × 10⁶  2.4

Vaccine candidates should be capable of providing, at low dose, long-term protection from challenge with a lethal dose of wt virus. The dose of (NA+HA)^(Min) required to protect 50% of vaccinated animals from subsequent lethal wild type challenge (defined as “protective dose 50”, PD₅₀) was determined. Groups of five Balb/c mice were vaccinated with a single dose of 10⁰, 10¹, or 10² PFU of (NA+HA)^(Min). 28 days after vaccination, the animals were challenged with 10⁵ PFU (3000×LD₅₀) of wt PR8 virus. As with the original infections, we monitored body weight and survival of the animals 14 days after challenge. Remarkably, although (NA+HA)^(Min) was highly attenuated in mice, it was also highly proficient at protecting against lethal challenge with wt virus. As little as 10 PFU of (NA+HA)^(Min) protected all five mice from lethal challenge (FIGS. 3C, 3D). The PD₅₀ value calculated by the method of Reed-Muench was only 2.4 PFU. (Table 5) To our knowledge this is the lowest reported protective dose of an experimental vaccine in a mouse model.

Vaccine safety and protective range was evaluated with various doses of either (NA+HA)^(Min) variant or wt PR8. As shown in FIG. 3E, a zone of five orders of magnitude (from 10 PFU to 10⁶ PFU) can be considered the “region of safety” of (NA+HA)^(Min) vaccination since all mice receiving increasing doses of “vaccine” within this region were protected from lethal challenge with wt virus. In contrast, the safe and effective region for wt PR8 was extremely limited (FIG. 3F).

Example 4 The Growth of (NA+HA)Min is Greatly Reduced in the Lungs of Vaccinated Mice

To determine parameters of the (NA+HA)^(Min) pathogenicity in vivo, groups of BALB/c mice were infected with 10⁴ PFU of wt PR8 or (NA+HA)^(Min). On day 1, 3, 5, 7, 9 and 11, three mice each from the wt and (NA+HA)^(Min) groups were euthanized, their lungs were homogenized, and virus titers in the homogenates were determined by plaque assays. As expected, wt PR8 replicated well, but even (NA+HA)^(Min) replicated noticeably in lungs of the vaccinated animals. Both PR8 and variant achieved maximum titers around day 3 (FIG. 4A) although there was a ˜100 fold difference in the titers between the two viruses. All wt PR8-infected mice died on day 5, whereas all (NA+HA)^(Min)-infected mice remained healthy. (NA+HA)^(Min) was eventually cleared at 8 to 9 days p.i. (FIG. 4A). When mice were inoculated at different doses, the (NA+HA)^(Min) titers were always 100-1000 fold lower in lungs when compare to those of wt PR8 on day 3 p.i. (FIG. 4B). Strikingly, at a vaccination dose of 10 PFU when (NA+HA)^(Min) barely replicated in the lungs of the animals, it nevertheless provided complete protection against wt PR8 challenge (FIGS. 4B and 3D). Interestingly, the attenuation of (NA+HA)^(Min) in mice correlates with the attenuation of (NA+HA)^(Min) in A549 cells (FIG. 1D).

Example 5 Cross Protection and Long Term Protection Induced by the (NA+HA)^(Min) Variant

The (NA+HA)^(Min) variant of PR8, which belongs to the influenza H1N1 subtype, was further tested for its capacity to cross protect animals against infections with a heterologous influenza virus strain, such as a mouse adapted H3N2 strain (A/Aichi/2/1968) (21). Groups of five BALB/c mice were vaccinated with (NA+HA)^(Min) virus at doses ranging from 10² to 10⁴ PFU and challenged 28 days post vaccination with 100×LD₅₀ doses of A/Aichi/2/1968 (H3N2) virus (1.5×10⁴ PFU). Remarkably, 1000 PFU of (NA+HA)^(Min) were sufficient to protect mice from the heterologous lethal challenge, corresponding to a PD₅₀ value of only 237 PFU (FIGS. 5A, 5B). A similar result was obtained when the vaccinated (NA+HA)^(Min) mice were challenged with a different strain of mouse adapted H3N2, A/Victoria/3/75. Again, as little as 1000 PFU of the H1N1 PR8-(NA+HA)^(Min) variant protected all mice from lethal challenge with 100×LD₅₀ dose (3.2×10⁴ PFU) of A/Victoria/3/75. The PD₅₀ of (NA+HA)^(Min) protecting against A/Victoria/3/75 (H3N2) was only 147 PFU (FIGS. 5C, 5D). Both results indicate that (NA+HA)^(Min) of H1N1 PR8 can induce a robust cross protective immune response in mice against H3N2 subtypes. .

(NA+HA)^(Min)-vaccinated animals were tested to determine whether they were protected against challenge after an extended period of time. Groups of five mice were vaccinated with different doses (10¹ to 10⁵ PFU) of (NA+HA)^(Min) and the animals were challenged seven months later with 10⁵ PFU of wt PR8. All vaccinated animals were completely protected without signs of disease (FIG. 8).

Example 6 The (NA+HA)^(Min) Variant Induces a Robust Antibody Response

The host response to (NA+HA)^(Min) inoculation suggested a strong host response, including adaptive immunity. Groups of five Balb/c mice were vaccinated with varying doses of (NA+HA)^(Min) or wt PR8 (see FIG. 6). Sera were collected on day 28 p.i., and antibody responses were determined by hemagglutination inhibition (HAI) assays performed according to the protocol in the WHO Manual on Animal Influenza Diagosis and Surveillance (23). The mice were challenged with a lethal dose of PR8 (10⁵ PFU). An HAI titer of 40 or more in the serum is generally considered to be protective (22). This level was reached with just 10¹ PFU of (NA+HA)^(Min) (FIG. 6) and protected vaccinated mice from challenge with 10⁵ PFU wt PR8 virus (FIG. 6).

Example 7 Virus Composition

Both WT and (NA+HA)^(Min) virus were purified by sucrose gradient. 5×10⁷ PFU of both viruses were loaded onto SDS gels followed by Commassie blue stain (0.1% Coomassie blue R250 for 45 min.) (FIG. 9A) or silver stain (Bio-Rad silver stain kit) (FIG. 9B and C) to detect virion protein composition. At the same PFU, WT virions contain more HA1 molecues than the (NA+HA)^(Min) virus, while the latter contains more M1 proteins.

WT and (NA+HA)^(Min) virus were also analyzed by Western blot. 2×10⁷ PFU of WT and (NA+HA)^(Min) viruses were loaded onto SDS-PAGE gels and analyzed for content of PB1, NP, HA2, and M1. At the same PFU of purified virions, the virus preparations have similar amounts of NP and PB1 protein. Purified WT virions, however, have more HA2 protein, while purified (NA+HA)^(Min) virions have more M1 protein. (FIG. 9D).

Example 8 Expression of Virus Proteins and mRNAs in Infected MDCK Cells

HA protein expression was measured by ³⁵S methionine incorporation. MDCK cells were infected with 10 MOI wild type PR8, or (NA+HA)^(Min) virus. At 3 h post infection, cells were starved for 45 min, and then labeled for 30 min. Following cell lysis, equal amounts of cell lysates were resolved by SDS PAGE and labeled proteins were visualized by autoradiography. Expression of the HA protein is notably reduced relative to other viral proteins in (NA+HA)^(Min) virus-infected cells. (FIG. 10A).

Viral mRNA in virus infected MDCK cells nucleus was analyzed by Northern blot. MDCK cells were infected with both WT and (NA+HA)^(Min) viruses at an MOI of 1. At 6 h, and 9 h post infection, cells were lysed using Life Technologies PARIS Kit. Nucleus and cytoplasmic portions were separated and mRNA were extracted from both portions. Northern blotting was performed using isolated mRNAs. The nuclear NP mRNA signals were relatively similar between WT and (NA+HA)^(Min) virus infected cells at all time points. Yet, WT virus infected cells, compared to (NA+HA)^(Min) viruses infected cells, contained more nuclear HA and NA mRNA, and less nuclear PB1 mRNA. (FIG. 10B)

Example 9 Passive Immunization by Serum Transfer from PR8-(NA+HA)^(Min) Vaccinated Mice Protects Naïve Mice from Homologous WT PR8 Challenge

Groups of five Balb/C mice were vaccinated with 10⁴ PFU (NA+HA)^(Min) virus or PBS. 28 days after vaccination mouse sera were collected, and transferred to five naïve Balb/C mice in a volume of 250 ul. 24 h post transfer, mice were challenged with 10⁵ PFU of WT PR8, corresponding to 3000×LD₅₀. All passively immunized mice survived and remained healthy upon challenge, while mock transferred mice died in 8 days. These results suggest that antibodies are the major mediator of immune protection induced by (NA+HA)^(Min) virus vaccination. (FIG. 11).

Example 10 Passive Immunization by Serum Transfer From PR8-(NA+HA)^(Min) Vaccinated Mice Protects Naïve Mice From Heterologous H3N2 Challenge

Groups of five Balb/C mice were infected with 3×10⁵ PFU H1N1-(NA+HA)^(Min) virus or PBS. On day 28, all mice were euthanized and their blood was collected. Sera were prepared on the same day and immediately transferred to groups of five naïve Balb/c mice (i.p injection with 250 μl of sera). 24 h post transfer, mice were challenged with 10×LD₅₀ of H1N1-WT PR8, H3N2 Aichi or H3N2 Victoria viruses. Their body weights (FIG. 12A) and survival rates (FIG. 12B) were monitored for 14 days post infection. 60% of sera transferred mice were protected from lethal H3N2 Aichi challenge, and survival times upon challenge of lethal H3N2 Victoria virus were extended.

Example 11 Cross Protection

Cross protection was investigated by assay of hemagglutination inhibition and neutralization. To determine inhibition of hemagglutination, groups of five Balb/C mice were vaccinated with 10²-10⁴ PFU of H1N1-(NA+HA)^(Min) virus. Sera were collected on day 28 p.i. Hemagglutination inhibition assays were performed by incubating the serum with H1N1 PR8, H3N2 Aichi or H3N2 Victoria virues. (FIG. 13A). H1N1-(NA+HA)^(Min) virus infected mice contain abundant anti-H1N1 HA antibodies with a HAI titer from 100-640. The sera, however, do not contain much of the anti-H3N2 HA antibodies, since the HAI titer are 40 regardless of the vaccine dose. This data suggests that survival of (NA+HA)^(Min) virus-vaccinated mice from heterologous challenge (as illustrated in Example 5) is mainly due to immunity not correlated with antibodies, such as cellular immunity.

To test neutralization, MDCK cells were seeded onto 96 well plate on day 0. 2 fold dilutions of sera from vaccinated mice were incubated with 100 TCID₅₀ viruses for 1 h and then added to pre-seeded MDCK cells on day 1. Cells were stained with crystal violet on day 4 to determine neutralization titers.

Groups of five Balb/C mice were vaccinated with 10⁵ PFU of H1N1-(NA+HA)^(Min) virus. Sera were collected on day 28 p.i. Neutralization assays were performed by incubating the sera with H1N1 PR8, H3N2 Aichi or H3N2 Victoria viruses. H1N1-(NA+HA)^(Min) virus infected mice were capable of neutralizing H1N1 PR8 with a neutralization titers above 1200. The sera, interestingly, were also able to neutralize H3N2 viruses. (FIG. 13B).

Example 12 Neuraminidase Encoded by (NA+HA)^(Min)

Viral neuraminidase cleaves terminal sialic acid residues from glycan structures on the surface of an infected cell, which promotes the release of progeny viruses. MDCK cells and MDCK-SIAT1 cells which overexpress overexpressing the α-2,6-Sialyltransferase, were infected with WT or (NA+HA)^(Min) viruses at MOI of 0.01. Virus titers were examined at 48 h p.i. In MDCK-SIAT1 cells, which overexpressed influenza receptor sialic acid, both WT and (NA+HA)^(Min) viruses grew better than MDCK cell lines. (FIG. 14). This indicates that (NA+HA)^(Min) virus comprises neuraminidase molecles encoded by NA^(Min) that cleave sialic acid residues normally.

Example 13 T and B Cell Responses in Lungs and Spleen

T cell responses in lungs. Groups of five Balb/C mice were with 10 PFU of WT (a dose close the LD₅₀ of this virus) or 10 PFU (NA+HA)^(Min) (a dose over 300,000-fold below the LD₅₀ for this virus). On day 7 post infection, mice were euthanized and their lungs were collected for flow cytometry. (NA+HA)^(Min) infected mice showed lower numbers of CD4+T and CD8+T cells than WT-infected mice, since (NA+HA)^(Min) infection is cleared by 7 days, while WT infection is still ongoing. (FIG. 15).

B cell responses in lungs. Groups of five Balb/C mice were infected with 10 PFU of WT or (NA+HA)^(Min) viruses. On day 7 post infection, mice were euthanized and their lungs were collected for flow cytometry. WT infected mice showed higher numbers of B cells than both the (NA+HA)^(Min) viruses and the mock group, indicating the WT viruses were much harder to clear than the other two. Yet, the percentage of CD45⁺ B cells in (NA+HA)^(Min) virus infected mice were similar, or slightly higher, than the WT PR8 infected mice, which indicates they share similar ability in inducing long term protective antibodies. (FIG. 16)

T cell responses in spleen. Groups of five Balb/C mice were infected with 10 PFU of WT or (NA+HA)^(Min) viruses. On day 7 post infection, mice were euthanized and their spleens were collected for flow cytometry. Both WT and (NA+HA)^(Min) virus infected mice showed higher number of CD4+T and CD8+T cells than the mock group, indicating a strong adaptive immune responses triggered by both viruses. (FIG. 17).

B cell responses in spleen. Groups of five Balb/C mice were infected with 10 PFU of WT or (NA+HA)^(Min) viruses. On day 7 post infection, mice were euthanized and their spleens were collected for flow cytometry. (NA+HA)^(Min) infected mice showed significantly higher numbers of B cells than mock group, indicating (NA+HA)^(Min) virus is highly efficient in inducing protective antibodies. (FIG. 18).

In summary, at 7 days post infection, the response to WT virus in lung tissue involved greater numbers of CD4+T, CD8+T and B cells to clear the viruses than the response to (NA+HA)^(Min). In spleen, (NA+HA)^(Min) and WT infected mice both showed elevated T and B cells, indicating strong adaptive immune responses. Also, the T cell proportion of cells in spleen responding to infection by (NA+HA)^(Min) was higher than the proportion responding to infection by WT virus. (FIG. 17).

Example 14 Flow Cytometry Analyses of Immune Cells Infiltrating Lung Tissue

Groups of five male Balb/C mice received 10⁴ PFU wild type PR8 (a lethal dose equal to 300-fold the LD₅₀ for this virus), 10⁴ PFU (NA+HA)^(Min) (a safe dose at least 300-fold below the LD₅₀ for this virus), or PBS. Note: A the chosen dose of 10⁴ PFU wild type PR8-infected mice invariably sucumb to the infection between 4 and 9 days. On day 3 post infection, lungs were collected and flow cytometry analyses were performed. FIG. 19 shows the results for various immune cells as follows: (A) CD45⁺ leukocytes, (B) CD45⁺ Ly6G^(high) polymorphonuclear leukocytes (PMN), (C) CD45⁺CD11c⁺ I-A^(d+) F4/80⁻ dendritic cells, (D) CD45⁺ NKp46⁺ natural killer cells, (E) CD45⁺CD11b⁺Ly6C^(high)Ly6G⁻ inflammatory monocytes, (F) CD45⁺ I-A^(d+) F4/80⁺ macrophages, (G) CD45⁺CD3⁺CD4⁺ T helper cells, (H) CD45⁺ CD19⁺ B cells, and (I) CD45⁺CD19⁺IgM⁺ B cells were monitored. Most notably (NA+HA)^(Min) infection induced a significantly higher amount of natural killer cells, implicated in viral clearance, as well as a reduced infiltration of PMN, which are known to be associated with immune induced lung damage following natural influenza virus infection. Thus the marked lack of PMN infiltration during (NA+HA)^(Min) infection may explain the high degree of attenuation (i.e the absence of virus induced disease and pathology) of (NA+HA)^(Min).

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SUPPLEMENTAL TABLE 1 Expected and Observed Codon Pair Frequencies and Codon Pair Scores for 14,795 Human Genes amino acid codon observed / pair pair expected observed expected CPS AA GCGGCG 630.04 2870 4.555 1.516 AA GCGGCC 2330.20 4032 1.730 0.548 AA GCTGCT 3727.41 5562 1.492 0.400 AA GCAGCA 2856.40 4196 1.469 0.385 AA GCAGCT 3262.97 4711 1.444 0.367 AA GCTGCA 3262.97 4357 1.335 0.289 AA GCTGCC 5667.77 7014 1.238 0.213 AA GCAGCC 4961.56 6033 1.216 0.196 AA GCAGCG 1341.51 1420 1.059 0.057 AA GCTGCG 1532.46 1533 1.000 0.000 AA GCGGCT 1532.46 1472 0.961 −0.040 AA GCCGCG 2330.20 2042 0.876 −0.132 AA GCGGCA 1341.51 1142 0.851 −0.161 AA GCCGCC 8618.21 5141 0.597 −0.517 AA GCCGCT 5667.77 1378 0.243 −1.414 AA GCCGCA 4961.56 1122 0.226 −1.487 AC GCCTGC 2333.61 3975 1.703 0.533 AC GCCTGT 1965.56 2436 1.239 0.215 AC GCGTGC 630.96 560 0.888 −0.119 AC GCTTGT 1292.65 1142 0.883 −0.124 AC GCATGT 1131.59 881 0.779 −0.250 AC GCGTGT 531.45 322 0.606 −0.501 AC GCTTGC 1534.70 894 0.583 −0.540 AC GCATGC 1343.47 554 0.412 −0.886 AD GCAGAT 2373.33 4215 1.776 0.574 AD GCTGAT 2711.15 3887 1.434 0.360 AD GCTGAC 3062.55 4374 1.428 0.356 AD GCGGAC 1259.11 1625 1.291 0.255 AD GCAGAC 2680.95 3395 1.266 0.236 AD GCGGAT 1114.64 839 0.753 −0.284 AD GCCGAC 4656.80 2726 0.585 −0.535 AD GCCGAT 4122.47 920 0.223 −1.500 AE GCAGAA 3517.48 5814 1.653 0.503 AE GCAGAG 4703.98 7094 1.508 0.411 AE GCGGAG 2209.23 3171 1.435 0.361 AE GCTGAG 5373.53 7362 1.370 0.315 AE GCTGAA 4018.14 5186 1.291 0.255 AE GCCGAG 8170.80 5082 0.622 −0.475 AE GCGGAA 1651.99 949 0.574 −0.554 AE GCCGAA 6109.85 1097 0.180 −1.717 AF GCCTTC 4447.90 7382 1.660 0.507 AF GCATTT 2237.22 2332 1.042 0.041 AF GCTTTT 2555.66 2580 1.010 0.009 AF GCCTTT 3886.04 3842 0.989 −0.011 AF GCTTTC 2925.16 2315 0.791 −0.234 AF GCGTTC 1202.63 636 0.529 −0.637 AF GCGTTT 1050.71 518 0.493 −0.707 AF GCATTC 2560.68 1261 0.492 −0.708 AG GCGGGC 1369.64 2638 1.926 0.655 AG GCGGGG 986.17 1738 1.762 0.567 AG GCTGGG 2398.67 3855 1.607 0.474 AG GCTGGT 1590.73 2524 1.587 0.462 AG GCTGGA 2457.02 3783 1.540 0.432 AG GCAGGA 2150.87 3074 1.429 0.357 AG GCAGGG 2099.79 2782 1.325 0.281 AG GCAGGT 1392.52 1748 1.255 0.227 AG GCTGGC 3331.38 3961 1.189 0.173 AG GCAGGC 2916.28 3119 1.070 0.067 AG GCGGGT 654.00 617 0.943 −0.058 AG GCGGGA 1010.16 793 0.785 −0.242 AG GCCGGG 3647.33 2240 0.614 −0.488 AG GCCGGC 5065.58 2977 0.588 −0.532 AG GCCGGT 2418.80 581 0.240 −1.426 AG GCCGGA 3736.06 795 0.213 −1.547 AH GCGCAC 748.29 983 1.314 0.273 AH GCCCAC 2767.53 3465 1.252 0.225 AH GCTCAT 1319.86 1471 1.115 0.108 AH GCACAT 1155.40 1122 0.971 −0.029 AH GCCCAT 2006.93 1827 0.910 −0.094 AH GCTCAC 1820.07 1526 0.838 −0.176 AH GCACAC 1593.29 1312 0.823 −0.194 AH GCGCAT 542.64 248 0.457 −0.783 AI GCCATC 3894.51 7798 2.002 0.694 AI GCCATT 3079.73 3761 1.221 0.200 AI GCAATA 815.43 924 1.133 0.125 AI GCAATT 1773.02 1684 0.950 −0.052 AI GCCATA 1416.41 1257 0.887 −0.119 AI GCTATT 2025.39 1709 0.844 −0.170 AI GCTATA 931.50 771 0.828 −0.189 AI GCTATC 2561.23 1194 0.466 −0.763 AI GCGATT 832.70 373 0.448 −0.803 AI GCAATC 2242.09 984 0.439 −0.824 AI GCGATA 382.97 149 0.389 −0.944 AI GCGATC 1053.00 404 0.384 −0.958 AK GCCAAG 5767.01 9818 1.702 0.532 AK GCAAAA 2563.57 3011 1.175 0.161 AK GCCAAA 4452.91 4794 1.077 0.074 AK GCAAAG 3320.10 3044 0.917 −0.087 AK GCTAAA 2928.46 2022 0.690 −0.370 AK GCGAAG 1559.29 765 0.491 −0.712 AK GCTAAG 3792.68 1725 0.455 −0.788 AK GCGAAA 1203.98 409 0.340 −1.080 AL GCGCTG 2369.16 4619 1.950 0.668 AL GCGCTC 1140.05 1765 1.548 0.437 AL GCTTTG 1873.51 2601 1.388 0.328 AL GCCCTG 8762.30 11409 1.302 0.264 AL GCCTTG 2848.79 3695 1.297 0.260 AL GCTTTA 1115.24 1385 1.242 0.217 AL GCCCTC 4216.45 4499 1.067 0.065 AL GCTCTT 1912.07 2038 1.066 0.064 AL GCATTA 976.28 986 1.010 0.010 AL GCTCTA 1031.16 940 0.912 −0.093 AL GCACTT 1673.82 1444 0.863 −0.148 AL GCATTG 1640.07 1364 0.832 −0.184 AL GCACTA 902.68 747 0.828 −0.189 AL GCGCTA 423.94 342 0.807 −0.215 AL GCCCTA 1567.95 1228 0.783 −0.244 AL GCTCTG 5762.53 4505 0.782 −0.246 AL GCCCTT 2907.42 2230 0.767 −0.265 AL GCTCTC 2772.95 2036 0.734 −0.309 AL GCCTTA 1695.80 1205 0.711 −0.342 AL GCACTG 5044.51 3522 0.698 −0.359 AL GCGTTG 770.26 476 0.618 −0.481 AL GCGCTT 786.11 459 0.584 −0.538 AL GCACTC 2427.43 1415 0.583 −0.540 AL GCGTTA 458.51 169 0.369 −0.998 AM GCCATG 4236.47 6521 1.539 0.431 AM GCAATG 2438.96 1900 0.779 −0.250 AM GCTATG 2786.11 1561 0.560 −0.579 AM GCGATG 1145.46 625 0.546 −0.606 AN GCCAAC 3190.28 5452 1.709 0.536 AN GCAAAT 1667.60 2282 1.368 0.314 AN GCCAAT 2896.62 3122 1.078 0.075 AN GCAAAC 1836.66 1512 0.823 −0.195 AN GCTAAT 1904.97 1356 0.712 −0.340 AN GCTAAC 2098.09 925 0.441 −0.819 AN GCGAAC 862.59 331 0.384 −0.958 AN GCGAAT 783.19 260 0.332 −1.103 AP GCGCCG 406.74 1172 2.881 1.058 AP GCGCCC 1122.56 2271 2.023 0.705 AP GCCCCG 1504.34 2335 1.552 0.440 AP GCTCCA 2360.19 2463 1.044 0.043 AP GCTCCT 2445.47 2548 1.042 0.041 AP GCCCCC 4151.78 3957 0.953 −0.048 AP GCACCT 2140.76 2028 0.947 −0.054 AP GCCCCA 3588.82 3371 0.939 −0.063 AP GCACCA 2066.10 1831 0.886 −0.121 AP GCACCC 2390.20 2111 0.883 −0.124 AP GCCCCT 3718.49 3269 0.879 −0.129 AP GCTCCC 2730.42 2384 0.873 −0.136 AP GCTCCG 989.33 773 0.781 −0.247 AP GCGCCT 1005.41 778 0.774 −0.256 AP GCACCG 866.06 571 0.659 −0.417 AP GCGCCA 970.35 595 0.613 −0.489 AQ GCCCAG 7143.67 9550 1.337 0.290 AQ GCGCAG 1931.51 2101 1.088 0.084 AQ GCACAA 1472.79 1416 0.961 −0.039 AQ GCTCAA 1682.42 1522 0.905 −0.100 AQ GCTCAG 4698.04 4141 0.881 −0.126 AQ GCACAG 4112.65 3374 0.820 −0.198 AQ GCCCAA 2558.23 1943 0.760 −0.275 AQ GCGCAA 691.70 244 0.353 −1.042 AR GCGCGC 580.17 1255 2.163 0.772 AR GCGCGG 634.54 1175 1.852 0.616 AR GCCCGG 2346.82 3946 1.681 0.520 AR GCCCGC 2145.76 3135 1.461 0.379 AR GCCAGG 2323.57 3242 1.395 0.333 AR GCAAGA 1362.59 1559 1.144 0.135 AR GCTCGA 836.64 943 1.127 0.120 AR GCCCGA 1272.16 1418 1.115 0.109 AR GCCCGT 918.67 935 1.018 0.018 AR GCTCGT 604.17 595 0.985 −0.015 AR GCCAGA 2366.81 2219 0.938 −0.064 AR GCTCGG 1543.39 1295 0.839 −0.175 AR GCGCGT 248.39 205 0.825 −0.192 AR GCAAGG 1337.69 1089 0.814 −0.206 AR GCGAGG 628.25 486 0.774 −0.257 AR GCACGA 732.39 533 0.728 −0.318 AR GCTCGC 1411.16 941 0.667 −0.405 AR GCGCGA 343.97 226 0.657 −0.420 AR GCACGT 528.89 338 0.639 −0.448 AR GCACGG 1351.08 859 0.636 −0.453 AR GCACGC 1235.33 619 0.501 −0.691 AR GCTAGA 1556.53 714 0.459 −0.779 AR GCGAGA 639.94 263 0.411 −0.889 AR GCTAGG 1528.10 487 0.319 −1.144 AS GCCTCG 963.41 1977 2.052 0.719 AS GCGTCG 260.49 465 1.785 0.579 AS GCCAGC 4127.58 6466 1.567 0.449 AS GCCTCC 3643.21 5443 1.494 0.401 AS GCTTCT 2084.25 2488 1.194 0.177 AS GCCAGT 2604.12 3085 1.185 0.169 AS GCATCT 1824.55 2154 1.181 0.166 AS GCTTCA 1684.99 1932 1.147 0.137 AS GCGTCC 985.05 1079 1.095 0.091 AS GCATCA 1475.04 1531 1.038 0.037 AS GCCTCT 3169.23 3235 1.021 0.021 AS GCCTCA 2562.14 2514 0.981 −0.019 AS GCTTCC 2395.96 2295 0.958 −0.043 AS GCAAGT 1499.21 1307 0.872 −0.137 AS GCTTCG 633.59 516 0.814 −0.205 AS GCATCC 2097.42 1658 0.790 −0.235 AS GCATCG 554.64 403 0.727 −0.319 AS GCGTCT 856.90 521 0.608 −0.498 AS GCGAGC 1116.02 595 0.533 −0.629 AS GCGTCA 692.75 319 0.460 −0.775 AS GCAAGC 2376.27 1080 0.454 −0.789 AS GCTAGT 1712.60 737 0.430 −0.843 AS GCGAGT 704.10 265 0.376 −0.977 AS GCTAGC 2714.51 673 0.248 −1.395 AT GCCACG 1262.40 2478 1.963 0.674 AT GCCACC 3842.98 6598 1.717 0.541 AT GCCACA 3111.04 4031 1.296 0.259 AT GCCACT 2751.18 3205 1.165 0.153 AT GCAACA 1791.05 1761 0.983 −0.017 AT GCGACG 341.33 329 0.964 −0.037 AT GCAACT 1583.87 1509 0.953 −0.048 AT GCTACT 1809.31 1395 0.771 −0.260 AT GCTACA 2045.98 1528 0.747 −0.292 AT GCGACC 1039.07 601 0.578 −0.547 AT GCAACC 2212.43 1259 0.569 −0.564 AT GCTACC 2527.34 1364 0.540 −0.617 AT GCAACG 726.77 384 0.528 −0.638 AT GCTACG 830.22 363 0.437 −0.827 AT GCGACT 743.87 308 0.414 −0.882 AT GCGACA 841.17 347 0.413 −0.885 AV GCTGTT 1736.99 3025 1.742 0.555 AV GCTGTG 4399.56 7279 1.654 0.503 AV GCTGTA 1127.89 1750 1.552 0.439 AV GCTGTC 2223.90 3351 1.507 0.410 AV GCAGTA 987.35 1401 1.419 0.350 AV GCGGTG 1808.80 2487 1.375 0.318 AV GCAGTT 1520.56 2087 1.373 0.317 AV GCAGTG 3851.36 4349 1.129 0.122 AV GCGGTC 914.32 883 0.966 −0.035 AV GCAGTC 1946.80 1806 0.928 −0.075 AV GCCGTG 6689.81 4322 0.646 −0.437 AV GCGGTT 714.13 423 0.592 −0.524 AV GCGGTA 463.71 270 0.582 −0.541 AV GCCGTC 3381.59 1798 0.532 −0.632 AV GCCGTT 2641.21 563 0.213 −1.546 AV GCCGTA 1715.03 329 0.192 −1.651 AW GCCTGG 2528.22 3848 1.522 0.420 AW GCGTGG 683.58 558 0.816 −0.203 AW GCTTGG 1662.69 1066 0.641 −0.445 AW GCATGG 1455.51 858 0.589 −0.529 AY GCCTAC 2643.77 4073 1.541 0.432 AY GCCTAT 2148.26 2457 1.144 0.134 AY GCTTAT 1412.81 1478 1.046 0.045 AY GCATAT 1236.77 1244 1.006 0.006 AY GCTTAC 1738.68 1139 0.655 −0.423 AY GCGTAC 714.83 429 0.600 −0.511 AY GCATAC 1522.04 868 0.570 −0.562 AY GCGTAT 580.85 310 0.534 −0.628 CA TGTGCT 1164.04 2021 1.736 0.552 CA TGTGCC 1769.99 2992 1.690 0.525 CA TGTGCA 1019.00 1708 1.676 0.517 CA TGTGCG 478.57 477 0.997 −0.003 CA TGCGCG 568.18 502 0.884 −0.124 CA TGCGCC 2101.42 1313 0.625 −0.470 CA TGCGCT 1382.00 368 0.266 −1.323 CA TGCGCA 1209.80 312 0.258 −1.355 CC TGCTGC 1534.17 2610 1.701 0.531 CC TGCTGT 1292.21 1571 1.216 0.195 CC TGTTGT 1088.41 529 0.486 −0.721 CC TGTTGC 1292.21 497 0.385 −0.956 CD TGTGAC 1920.20 3470 1.807 0.592 CD TGTGAT 1699.87 2853 1.678 0.518 CD TGCGAC 2279.75 1134 0.497 −0.698 CD TGCGAT 2018.17 461 0.228 −1.477 CE TGTGAA 1901.69 3636 1.912 0.648 CE TGTGAG 2543.16 3935 1.547 0.437 CE TGCGAG 3019.37 1709 0.566 −0.569 CE TGCGAA 2257.78 442 0.196 −1.631 CF TGCTTC 1891.74 2684 1.419 0.350 CF TGCTTT 1652.78 1685 1.019 0.019 CF TGTTTT 1392.11 1096 0.787 −0.239 CF TGTTTC 1593.38 1065 0.668 −0.403 CG TGTGGG 1594.78 3240 2.032 0.709 CG TGTGGA 1633.57 2846 1.742 0.555 CG TGTGGT 1057.61 1627 1.538 0.431 CG TGTGGC 2214.90 3133 1.415 0.347 CG TGCGGG 1893.40 1137 0.601 −0.510 CG TGCGGC 2629.63 1461 0.556 −0.588 CG TGCGGT 1255.64 344 0.274 −1.295 CG TGCGGA 1939.46 431 0.222 −1.504 CH TGCCAC 1618.50 2144 1.325 0.281 CH TGCCAT 1173.68 1253 1.068 0.065 CH TGTCAT 988.58 831 0.841 −0.174 CH TGTCAC 1363.24 916 0.672 −0.398 CI TGCATC 1821.04 2813 1.545 0.435 CI TGCATT 1440.05 1579 1.096 0.092 CI TGCATA 662.30 576 0.870 −0.140 CI TGTATA 557.84 474 0.850 −0.163 CI TGTATT 1212.94 927 0.764 −0.269 CI TGTATC 1533.83 859 0.560 −0.580 CK TGCAAG 2777.53 3348 1.205 0.187 CK TGCAAA 2144.62 2441 1.138 0.129 CK TGTAAA 1806.38 1770 0.980 −0.020 CK TGTAAG 2339.47 1509 0.645 −0.438 CL TGCCTC 1722.14 2468 1.433 0.360 CL TGCCTG 3578.83 4525 1.264 0.235 CL TGTTTA 583.38 704 1.207 0.188 CL TGCCTT 1187.49 1384 1.165 0.153 CL TGTTTG 980.04 1079 1.101 0.096 CL TGCTTG 1163.55 1179 1.013 0.013 CL TGTCTT 1000.21 940 0.940 −0.062 CL TGCCTA 640.41 585 0.913 −0.090 CL TGTCTA 539.40 481 0.892 −0.115 CL TGCTTA 692.62 565 0.816 −0.204 CL TGTCTC 1450.53 1010 0.696 −0.362 CL TGTCTG 3014.39 1633 0.542 −0.613 CM TGCATG 1518.22 1979 1.304 0.265 CM TGTATG 1278.78 818 0.640 −0.447 CN TGCAAC 1825.04 2351 1.288 0.253 CN TGCAAT 1657.05 1636 0.987 −0.013 CN TGTAAT 1395.71 1349 0.967 −0.034 CN TGTAAC 1537.20 1079 0.702 −0.354 CP TGCCCG 687.28 978 1.423 0.353 CP TGCCCC 1896.80 2279 1.201 0.184 CP TGCCCA 1639.61 1728 1.054 0.053 CP TGCCCT 1698.85 1690 0.995 −0.005 CP TGTCCT 1430.91 1333 0.932 −0.071 CP TGTCCA 1381.01 1263 0.915 −0.089 CP TGTCCC 1597.65 1369 0.857 −0.154 CP TGTCCG 578.88 271 0.468 −0.759 CQ TGCCAG 3338.89 4321 1.294 0.258 CQ TGCCAA 1195.69 1319 1.103 0.098 CQ TGTCAA 1007.11 905 0.899 −0.107 CQ TGTCAG 2812.30 1809 0.643 −0.441 CR TGCCGC 1031.52 1860 1.803 0.590 CR TGCCGG 1128.18 1543 1.368 0.313 CR TGCAGG 1117.00 1450 1.298 0.261 CR TGCCGT 441.63 541 1.225 0.203 CR TGCCGA 611.56 742 1.213 0.193 CR TGCAGA 1137.78 1252 1.100 0.096 CR TGTCGA 515.11 458 0.889 −0.118 CR TGTCGT 371.98 308 0.828 −0.189 CR TGTAGA 958.34 570 0.595 −0.520 CR TGTCGC 868.83 497 0.572 −0.559 CR TGTCGG 950.24 463 0.487 −0.719 CR TGTAGG 940.83 389 0.413 −0.883 CS TGCAGC 1990.73 3150 1.582 0.459 CS TGCTCC 1757.12 2397 1.364 0.311 CS TGCAGT 1255.97 1701 1.354 0.303 CS TGCTCG 464.65 571 1.229 0.206 CS TGTTCT 1287.45 1184 0.920 −0.084 CS TGCTCT 1528.52 1393 0.911 −0.093 CS TGTTCA 1040.83 932 0.895 −0.110 CS TGCTCA 1235.72 1079 0.873 −0.136 CS TGTTCC 1479.99 1102 0.745 −0.295 CS TGTAGT 1057.88 699 0.661 −0.414 CS TGTTCG 391.37 192 0.491 −0.712 CS TGTAGC 1676.76 767 0.457 −0.782 CT TGCACG 535.88 829 1.547 0.436 CT TGCACC 1631.31 2321 1.423 0.353 CT TGCACA 1320.60 1508 1.142 0.133 CT TGCACT 1167.85 1185 1.015 0.015 CT TGTACT 983.66 802 0.815 −0.204 CT TGTACA 1112.32 830 0.746 −0.293 CT TGTACC 1374.02 942 0.686 −0.377 CT TGTACG 451.36 160 0.354 −1.037 CV TGTGTC 1064.94 1821 1.710 0.536 CV TGTGTT 831.78 1383 1.663 0.508 CV TGTGTA 540.10 866 1.603 0.472 CV TGTGTG 2106.78 3241 1.538 0.431 CV TGCGTG 2501.27 1537 0.614 −0.487 CV TGCGTC 1264.35 734 0.581 −0.544 CV TGCGTT 987.53 219 0.222 −1.506 CV TGCGTA 641.24 137 0.214 −1.543 CW TGCTGG 1275.05 1842 1.445 0.368 CW TGTTGG 1073.95 507 0.472 −0.751 CY TGCTAC 1379.34 1995 1.446 0.369 CY TGCTAT 1120.82 1170 1.044 0.043 CY TGTTAT 944.05 653 0.692 −0.369 CY TGTTAC 1161.80 788 0.678 −0.388 DA GATGCT 2675.13 5292 1.978 0.682 DA GATGCA 2341.80 3898 1.665 0.510 DA GATGCC 4067.71 5983 1.471 0.386 DA GACGCG 1242.39 1116 0.898 −0.107 DA GATGCG 1099.83 972 0.884 −0.124 DA GACGCC 4594.94 2668 0.581 −0.544 DA GACGCA 2645.34 852 0.322 −1.133 DA GACGCT 3021.87 908 0.300 −1.202 DC GACTGC 2386.86 3465 1.452 0.373 DC GACTGT 2010.41 2804 1.395 0.333 DC GATTGT 1779.74 1163 0.653 −0.425 DC GATTGC 2112.99 858 0.406 −0.901 DD GATGAT 4271.42 7846 1.837 0.608 DD GATGAC 4825.06 7181 1.488 0.398 DD GACGAC 5450.46 2965 0.544 −0.609 DD GACGAT 4825.06 1380 0.286 −1.252 DE GATGAA 5114.33 10045 1.964 0.675 DE GATGAG 6839.48 9573 1.400 0.336 DE GACGAG 7725.97 4498 0.582 −0.541 DE GACGAA 5777.22 1341 0.232 −1.461 DF GACTTC 4696.28 6094 1.298 0.261 DF GACTTT 4103.05 4250 1.036 0.035 DF GATTTT 3632.26 3485 0.959 −0.041 DF GATTTC 4157.42 2760 0.664 −0.410 DG GATGGT 1910.36 3443 1.802 0.589 DG GATGGA 2950.72 5133 1.740 0.554 DG GATGGG 2880.65 4437 1.540 0.432 DG GATGGC 4000.77 5419 1.354 0.303 DG GACGGC 4519.33 2987 0.661 −0.414 DG GACGGG 3254.02 1979 0.608 −0.497 DG GACGGT 2157.97 723 0.335 −1.094 DG GACGGA 3333.18 886 0.266 −1.325 DH GACCAC 2653.74 3480 1.311 0.271 DH GACCAT 1924.41 2014 1.047 0.046 DH GATCAT 1703.60 1623 0.953 −0.048 DH GATCAC 2349.25 1514 0.644 −0.439 DI GACATC 4715.94 6532 1.385 0.326 DI GACATT 3729.31 4087 1.096 0.092 DI GATATT 3301.40 3271 0.991 −0.009 DI GATATA 1518.36 1495 0.985 −0.016 DI GACATA 1715.16 1565 0.912 −0.092 DI GATATC 4174.83 2205 0.528 −0.638 DK GACAAG 5562.52 7324 1.317 0.275 DK GACAAA 4295.02 4794 1.116 0.110 DK GATAAA 3802.20 3855 1.014 0.014 DK GATAAG 4924.27 2611 0.530 −0.634 DL GACCTC 3785.97 5029 1.328 0.284 DL GACTTG 2557.95 3396 1.328 0.283 DL GATTTA 1347.95 1740 1.291 0.255 DL GACCTG 7867.71 9796 1.245 0.219 DL GATTTG 2264.44 2687 1.187 0.171 DL GACCTT 2610.58 2774 1.063 0.061 DL GATCTT 2311.04 2416 1.045 0.044 DL GACCTA 1407.87 1416 1.006 0.006 DL GACTTA 1522.66 1403 0.921 −0.082 DL GATCTA 1246.33 1020 0.818 −0.200 DL GATCTC 3351.56 2214 0.661 −0.415 DL GATCTG 6964.95 3348 0.481 −0.733 DM GACATG 4089.63 5411 1.323 0.280 DM GATATG 3620.37 2299 0.635 −0.454 DN GACAAC 3511.00 4849 1.381 0.323 DN GACAAT 3187.82 3349 1.051 0.049 DN GATAAT 2822.05 2549 0.903 −0.102 DN GATAAC 3108.14 1882 0.606 −0.502 DP GACCCC 3732.11 5119 1.372 0.316 DP GACCCG 1352.28 1692 1.251 0.224 DP GACCCT 3342.62 3700 1.107 0.102 DP GATCCT 2959.08 3111 1.051 0.050 DP GACCCA 3226.05 3205 0.993 −0.007 DP GATCCA 2855.89 2349 0.823 −0.195 DP GATCCC 3303.88 2338 0.708 −0.346 DP GATCCG 1197.11 455 0.380 −0.967 DQ GACCAG 5250.37 6524 1.243 0.217 DQ GACCAA 1880.22 2169 1.154 0.143 DQ GATCAA 1664.48 1808 1.086 0.083 DQ GATCAG 4647.93 2942 0.633 −0.457 DR GACCGC 1807.77 2634 1.457 0.376 DR GACAGA 1994.00 2869 1.439 0.364 DR GACAGG 1957.57 2730 1.395 0.333 DR GACCGT 773.97 1029 1.330 0.285 DR GACCGG 1977.16 2568 1.299 0.261 DR GACCGA 1071.78 1292 1.205 0.187 DR GATCGA 948.80 923 0.973 −0.028 DR GATCGT 685.16 626 0.914 −0.090 DR GATAGA 1765.20 1123 0.636 −0.452 DR GATCGG 1750.30 859 0.491 −0.712 DR GATCGC 1600.34 754 0.471 −0.753 DR GATAGG 1732.96 658 0.380 −0.968 DS GACTCG 918.57 1527 1.662 0.508 DS GACAGC 3935.48 6143 1.561 0.445 DS GACAGT 2482.92 3657 1.473 0.387 DS GATTCT 2675.01 2968 1.110 0.104 DS GACTCC 3473.65 3800 1.094 0.090 DS GATTCA 2162.59 2129 0.984 −0.016 DS GACTCA 2442.89 2382 0.975 −0.025 DS GACTCT 3021.73 2910 0.963 −0.038 DS GATTCC 3075.07 2186 0.711 −0.341 DS GATAGT 2198.02 1355 0.616 −0.484 DS GATTCG 813.17 414 0.509 −0.675 DS GATAGC 3483.91 1212 0.348 −1.056 DT GACACG 1110.58 1842 1.659 0.506 DT GACACC 3380.79 4666 1.380 0.322 DT GACACA 2736.88 3538 1.293 0.257 DT GACACT 2420.30 2688 1.111 0.105 DT GATACT 2142.59 1731 0.808 −0.213 DT GATACA 2422.85 1788 0.738 −0.304 DT GATACC 2992.87 1586 0.530 −0.635 DT GATACG 983.15 351 0.357 −1.030 DV GATGTT 1957.96 3699 1.889 0.636 DV GATGTA 1271.37 2214 1.741 0.555 DV GATGTC 2506.81 3869 1.543 0.434 DV GATGTG 4959.23 6668 1.345 0.296 DV GACGTG 5602.02 3616 0.645 −0.438 DV GACGTC 2831.73 1654 0.584 −0.538 DV GACGTT 2211.73 672 0.304 −1.191 DV GACGTA 1436.16 385 0.268 −1.316 DW GACTGG 2619.27 3853 1.471 0.386 DW GATTGG 2318.73 1085 0.468 −0.759 DY GACTAC 3307.71 3930 1.188 0.172 DY GATTAT 2379.36 2608 1.096 0.092 DY GACTAT 2687.76 2853 1.061 0.060 DY GATTAC 2928.18 1912 0.653 −0.426 EA GAGGCG 2437.29 3179 1.304 0.266 EA GAAGCA 3880.59 4844 1.248 0.222 EA GAAGCT 4432.94 5143 1.160 0.149 EA GAGGCC 9014.27 9805 1.088 0.084 EA GAGGCT 5928.25 5314 0.896 −0.109 EA GAGGCA 5189.57 4530 0.873 −0.136 EA GAAGCC 6740.57 5649 0.838 −0.177 EA GAAGCG 1822.52 982 0.539 −0.618 EC GAATGT 2182.58 3541 1.622 0.484 EC GAGTGT 2918.80 2792 0.957 −0.044 EC GAGTGC 3465.35 2987 0.862 −0.149 EC GAATGC 2591.27 1838 0.709 −0.343 ED GAAGAT 6605.82 9691 1.467 0.383 ED GAGGAC 9979.09 9684 0.970 −0.030 ED GAAGAC 7462.02 6820 0.914 −0.090 ED GAGGAT 8834.07 6686 0.757 −0.279 EE GAAGAA 10747.11 14461 1.346 0.297 EE GAGGAG 19220.31 21731 1.131 0.123 EE GAAGAG 14372.29 11875 0.826 −0.191 EE GAGGAA 14372.29 10645 0.741 −0.300 EF GAATTT 3136.91 4237 1.351 0.301 EF GAGTTC 4801.58 4739 0.987 −0.013 EF GAGTTT 4195.05 4095 0.976 −0.024 EF GAATTC 3590.46 2653 0.739 −0.303 EG GAAGGA 3358.73 5032 1.498 0.404 EG GAAGGT 2174.51 2839 1.306 0.267 EG GAAGGG 3278.97 3559 1.085 0.082 EG GAGGGC 6090.10 6505 1.068 0.066 EG GAAGGC 4553.97 4340 0.953 −0.048 EG GAGGGG 4385.02 3795 0.865 −0.145 EG GAGGGT 2908.01 2378 0.818 −0.201 EG GAGGGA 4491.69 2793 0.622 −0.475 EH GAACAT 2017.28 2539 1.259 0.230 EH GAGCAC 3720.16 4190 1.126 0.119 EH GAGCAT 2697.74 2448 0.907 −0.097 EH GAACAC 2781.81 2040 0.733 −0.310 EI GAAATA 1687.78 3007 1.782 0.578 EI GAAATT 3669.78 4788 1.305 0.266 EI GAGATC 6206.03 6191 0.998 −0.002 EI GAGATT 4907.66 3978 0.811 −0.210 EI GAGATA 2257.09 1785 0.791 −0.235 EI GAAATC 4640.66 3620 0.780 −0.248 EK GAGAAG 12729.57 15133 1.189 0.173 EK GAAAAA 7349.75 7522 1.023 0.023 EK GAGAAA 9828.94 9127 0.929 −0.074 EK GAAAAG 9518.74 7645 0.803 −0.219 EL GAGCTG 10945.64 15625 1.428 0.356 EL GAATTA 1584.03 2256 1.424 0.354 EL GAACTA 1464.61 1830 1.249 0.223 EL GAACTT 2715.79 3371 1.241 0.216 EL GAGCTC 5267.08 5877 1.116 0.110 EL GAGCTA 1958.64 2049 1.046 0.045 EL GAATTG 2661.03 2335 0.877 −0.131 EL GAGCTT 3631.87 3084 0.849 −0.164 EL GAGTTG 3558.64 2719 0.764 −0.269 EL GAACTC 3938.54 2632 0.668 −0.403 EL GAGTTA 2118.35 1357 0.641 −0.445 EL GAACTG 8184.78 4894 0.598 −0.514 EM GAAATG 4983.92 5010 1.005 0.005 EM GAGATG 6665.08 6639 0.996 −0.004 EN GAAAAT 4791.73 6977 1.456 0.376 EN GAGAAC 7057.70 6756 0.957 −0.044 EN GAAAAC 5277.51 4930 0.934 −0.068 EN GAGAAT 6408.07 4872 0.760 −0.274 EP GAGCCG 1650.94 2438 1.477 0.390 EP GAGCCC 4556.38 6270 1.376 0.319 EP GAGCCT 4080.86 4236 1.038 0.037 EP GAGCCA 3938.55 4067 1.033 0.032 EP GAACCA 2945.12 2684 0.911 −0.093 EP GAACCT 3051.53 2547 0.835 −0.181 EP GAACCC 3407.10 2106 0.618 −0.481 EP GAACCG 1234.52 517 0.419 −0.870 EQ GAACAA 2579.50 3396 1.317 0.275 EQ GAGCAG 9632.80 11185 1.161 0.149 EQ GAGCAA 3449.61 3185 0.923 −0.080 EQ GAACAG 7203.08 5099 0.708 −0.345 ER GAAAGA 2650.27 3769 1.422 0.352 ER GAGAGG 3479.50 4315 1.240 0.215 ER GAGCGG 3514.32 4356 1.240 0.215 ER GAGCGC 3213.23 3682 1.146 0.136 ER GAAAGG 2601.85 2679 1.030 0.029 ER GAGAGA 3544.25 3633 1.025 0.025 ER GAGCGT 1375.70 1286 0.935 −0.067 ER GAACGT 1028.70 894 0.869 −0.140 ER GAACGA 1424.52 1188 0.834 −0.182 ER GAGCGA 1905.04 1562 0.820 −0.199 ER GAACGG 2627.88 1333 0.507 −0.679 ER GAACGC 2402.74 1071 0.446 −0.808 ES GAAAGT 2081.93 3138 1.507 0.410 ES GAGAGC 4413.03 5786 1.311 0.271 ES GAGAGT 2784.21 3237 1.163 0.151 ES GAGTCG 1030.03 1174 1.140 0.131 ES GAATCT 2533.73 2812 1.110 0.104 ES GAATCA 2048.37 2131 1.040 0.040 ES GAAAGC 3299.91 2880 0.873 −0.136 ES GAGTCC 3895.16 3392 0.871 −0.138 ES GAGTCT 3388.40 2799 0.826 −0.191 ES GAGTCA 2739.33 2198 0.802 −0.220 ES GAATCC 2912.67 1943 0.667 −0.405 ES GAATCG 770.22 407 0.528 −0.638 ET GAGACG 1658.42 2190 1.321 0.278 ET GAAACA 3056.09 3851 1.260 0.231 ET GAAACT 2702.59 3224 1.193 0.176 ET GAGACC 5048.51 5514 1.092 0.088 ET GAGACA 4086.97 3619 0.885 −0.122 ET GAGACT 3614.21 3028 0.838 −0.177 ET GAAACC 3775.11 2950 0.781 −0.247 ET GAAACG 1240.11 806 0.650 −0.431 EV GAAGTA 1580.16 2675 1.693 0.526 EV GAAGTT 2433.50 3724 1.530 0.425 EV GAGGTG 8242.83 9074 1.101 0.096 EV GAAGTC 3115.66 2860 0.918 −0.086 EV GAGGTC 4166.62 3741 0.898 −0.108 EV GAAGTG 6163.71 5122 0.831 −0.185 EV GAGGTT 3254.36 2359 0.725 −0.322 EV GAGGTA 2113.17 1515 0.717 −0.333 EW GAGTGG 3085.08 3238 1.050 0.048 EW GAATGG 2306.92 2154 0.934 −0.069 EY GAATAT 2307.55 3428 1.486 0.396 EY GAGTAC 3797.72 3796 1.000 0.000 EY GAGTAT 3085.93 2596 0.841 −0.173 EY GAATAC 2839.80 2211 0.779 −0.250 FA TTTGCA 1643.98 3299 2.007 0.696 FA TTTGCT 1877.98 3746 1.995 0.690 FA TTTGCC 2855.59 4348 1.523 0.420 FA TTTGCG 772.10 622 0.806 −0.216 FA TTCGCG 883.73 598 0.677 −0.391 FA TTCGCC 3268.46 1802 0.551 −0.595 FA TTCGCT 2149.50 516 0.240 −1.427 FA TTCGCA 1881.67 402 0.214 −1.543 FC TTCTGC 2058.60 3045 1.479 0.391 FC TTCTGT 1733.93 2055 1.185 0.170 FC TTTTGT 1514.90 1159 0.765 −0.268 FC TTTTGC 1798.56 847 0.471 −0.753 FD TTTGAT 2786.65 5380 1.931 0.658 FD TTTGAC 3147.84 4737 1.505 0.409 FD TTCGAC 3602.96 1746 0.485 −0.724 FD TTCGAT 3189.55 864 0.271 −1.306 FE TTTGAA 3016.02 6247 2.071 0.728 FE TTTGAG 4033.37 6066 1.504 0.408 FE TTCGAG 4616.53 2165 0.469 −0.757 FE TTCGAA 3452.08 640 0.185 −1.685 FF TTCTTC 3429.53 5168 1.507 0.410 FF TTCTTT 2996.32 2989 0.998 −0.002 FF TTTTTT 2617.83 1937 0.740 −0.301 FF TTTTTC 2996.32 1946 0.649 −0.432 FG TTTGGA 2068.21 4271 2.065 0.725 FG TTTGGT 1339.00 2552 1.906 0.645 FG TTTGGG 2019.09 3449 1.708 0.535 FG TTTGGC 2804.20 3462 1.235 0.211 FG TTCGGG 2311.02 1292 0.559 −0.581 FG TTCGGC 3209.64 1648 0.513 −0.667 FG TTCGGT 1532.60 419 0.273 −1.297 FG TTCGGA 2367.24 558 0.236 −1.445 FH TTCCAC 2463.48 3200 1.299 0.262 FH TTTCAT 1560.78 1697 1.087 0.084 FH TTCCAT 1786.44 1866 1.045 0.044 FH TTTCAC 2152.30 1200 0.558 −0.584 FI TTCATC 3454.46 5156 1.493 0.400 FI TTCATT 2731.75 2953 1.081 0.078 FI TTTATT 2386.67 2296 0.962 −0.039 FI TTTATA 1097.66 950 0.865 −0.144 FI TTCATA 1256.36 1035 0.824 −0.194 FI TTTATC 3018.10 1555 0.515 −0.663 FK TTCAAG 4090.45 5137 1.256 0.228 FK TTCAAA 3158.38 3245 1.027 0.027 FK TTTAAA 2759.42 2762 1.001 0.001 FK TTTAAG 3573.75 2438 0.682 −0.382 FL TTCCTC 3228.53 4426 1.371 0.315 FL TTCCTG 6709.28 8734 1.302 0.264 FL TTTTTA 1134.45 1334 1.176 0.162 FL TTTCTT 1945.00 2267 1.166 0.153 FL TTCCTA 1200.58 1280 1.066 0.064 FL TTTCTA 1048.92 1087 1.036 0.036 FL TTCTTG 2181.32 2239 1.026 0.026 FL TTCCTT 2226.21 2150 0.966 −0.035 FL TTTTTG 1905.78 1799 0.944 −0.058 FL TTCTTA 1298.47 1144 0.881 −0.127 FL TTTCTC 2820.70 1904 0.675 −0.393 FL TTTCTG 5861.77 3197 0.545 −0.606 FM TTCATG 2804.11 3662 1.306 0.267 FM TTTATG 2449.89 1592 0.650 −0.431 FN TTCAAC 2855.47 3919 1.372 0.317 FN TTTAAT 2265.13 2185 0.965 −0.036 FN TTCAAT 2592.63 2456 0.947 −0.054 FN TTTAAC 2494.77 1648 0.661 −0.415 FP TTCCCG 961.40 1205 1.253 0.226 FP TTTCCT 2076.25 2539 1.223 0.201 FP TTCCCC 2653.35 3099 1.168 0.155 FP TTTCCA 2003.85 2141 1.068 0.066 FP TTCCCA 2293.57 2310 1.007 0.007 FP TTCCCT 2376.44 2379 1.001 0.001 FP TTTCCC 2318.18 1529 0.660 −0.416 FP TTTCCG 839.96 321 0.382 −0.962 FQ TTCCAG 5468.69 7069 1.293 0.257 FQ TTTCAA 1711.02 1803 1.054 0.052 FQ TTCCAA 1958.40 1980 1.011 0.011 FQ TTTCAG 4777.89 3064 0.641 −0.444 FR TTCCGC 1531.47 2588 1.690 0.525 FR TTCCGA 907.97 1410 1.553 0.440 FR TTCCGG 1674.97 2451 1.463 0.381 FR TTCCGT 655.68 893 1.362 0.309 FR TTCAGA 1689.24 1852 1.096 0.092 FR TTCAGG 1658.38 1810 1.091 0.087 FR TTTCGA 793.28 850 1.072 0.069 FR TTTCGT 572.85 490 0.855 −0.156 FR TTTAGA 1475.86 947 0.642 −0.444 FR TTTAGG 1448.90 691 0.477 −0.740 FR TTTCGG 1463.39 688 0.470 −0.755 FR TTTCGC 1338.02 540 0.404 −0.907 FS TTCTCC 2990.83 4507 1.507 0.410 FS TTCAGC 3388.47 4577 1.351 0.301 FS TTCAGT 2137.80 2692 1.259 0.231 FS TTCTCG 790.89 910 1.151 0.140 FS TTTTCT 2273.08 2536 1.116 0.109 FS TTCTCT 2601.73 2741 1.054 0.052 FS TTTTCA 1837.65 1903 1.036 0.035 FS TTCTCA 2103.34 1997 0.949 −0.052 FS TTTTCC 2613.03 1872 0.716 −0.334 FS TTTAGT 1867.76 1201 0.643 −0.442 FS TTTTCG 690.99 258 0.373 −0.985 FS TTTAGC 2960.44 1062 0.359 −1.025 FT TTCACC 2909.29 4513 1.551 0.439 FT TTCACG 955.69 1315 1.376 0.319 FT TTCACT 2082.75 2494 1.197 0.180 FT TTCACA 2355.18 2372 1.007 0.007 FT TTTACT 1819.66 1622 0.891 −0.115 FT TTTACA 2057.68 1485 0.722 −0.326 FT TTTACC 2541.79 1495 0.588 −0.531 FT TTTACG 834.97 261 0.313 −1.163 FV TTTGTA 912.19 1711 1.876 0.629 FV TTTGTT 1404.80 2620 1.865 0.623 FV TTTGTC 1798.60 2635 1.465 0.382 FV TTTGTG 3558.17 5206 1.463 0.381 FV TTCGTG 4072.62 2589 0.636 −0.453 FV TTCGTC 2058.64 1086 0.528 −0.640 FV TTCGTT 1607.91 386 0.240 −1.427 FV TTCGTA 1044.07 224 0.215 −1.539 FW TTCTGG 2126.30 2834 1.333 0.287 FW TTTTGG 1857.70 1150 0.619 −0.480 FY TTCTAC 2720.70 3710 1.364 0.310 FY TTTTAT 1931.51 2003 1.037 0.036 FY TTCTAT 2210.77 2145 0.970 −0.030 FY TTTTAC 2377.02 1382 0.581 −0.542 GA GGTGCT 1531.20 2505 1.636 0.492 GA GGGGCG 949.27 1433 1.510 0.412 GA GGGGCC 3510.85 5061 1.442 0.366 GA GGTGCC 2328.29 3109 1.335 0.289 GA GGAGCA 2070.38 2678 1.293 0.257 GA GGTGCA 1340.41 1715 1.279 0.246 GA GGCGCG 1318.38 1659 1.258 0.230 GA GGAGCT 2365.08 2975 1.258 0.229 GA GGGGCT 2308.91 2850 1.234 0.211 GA GGAGCC 3596.25 3845 1.069 0.067 GA GGGGCA 2021.22 2074 1.026 0.026 GA GGTGCG 629.52 501 0.796 −0.228 GA GGAGCG 972.36 712 0.732 −0.312 GA GGCGCC 4876.02 3121 0.640 −0.446 GA GGCGCT 3206.72 906 0.283 −1.264 GA GGCGCA 2807.15 688 0.245 −1.406 GC GGCTGC 1888.96 4102 2.172 0.775 GC GGCTGT 1591.04 2360 1.483 0.394 GC GGTTGT 759.72 658 0.866 −0.144 GC GGATGT 1173.45 793 0.676 −0.392 GC GGTTGC 901.97 523 0.580 −0.545 GC GGATGC 1393.18 655 0.470 −0.755 GC GGGTGC 1360.09 628 0.462 −0.773 GC GGGTGT 1145.59 495 0.432 −0.839 GD GGGGAC 3126.50 4967 1.589 0.463 GD GGTGAT 1835.49 2621 1.428 0.356 GD GGTGAC 2073.40 2960 1.428 0.356 GD GGAGAT 2835.09 3829 1.351 0.301 GD GGAGAC 3202.56 4240 1.324 0.281 GD GGGGAT 2767.76 2575 0.930 −0.072 GD GGCGAC 4342.22 1955 0.450 −0.798 GD GGCGAT 3843.98 880 0.229 −1.474 GE GGAGAA 3433.99 5903 1.719 0.542 GE GGGGAG 4483.27 6552 1.461 0.379 GE GGTGAA 2223.23 3248 1.461 0.379 GE GGAGAG 4592.33 5961 1.298 0.261 GE GGTGAG 2973.17 2988 1.005 0.005 GE GGGGAA 3352.44 3041 0.907 −0.098 GE GGCGAG 6226.56 3530 0.567 −0.568 GE GGCGAA 4656.01 718 0.154 −1.869 GF GGCTTC 3466.22 6121 1.766 0.569 GF GGATTT 2233.54 2666 1.194 0.177 GF GGTTTT 1446.04 1665 1.151 0.141 GF GGCTTT 3028.37 3201 1.057 0.055 GF GGTTTC 1655.11 1548 0.935 −0.067 GF GGATTC 2556.47 1534 0.600 −0.511 GF GGGTTT 2180.50 1244 0.571 −0.561 GF GGGTTC 2495.76 1083 0.434 −0.835 GG GGTGGT 1061.28 2286 2.154 0.767 GG GGTGGC 2222.59 3657 1.645 0.498 GG GGTGGA 1639.25 2618 1.597 0.468 GG GGAGGA 2531.97 3609 1.425 0.354 GG GGTGGG 1600.32 2267 1.417 0.348 GG GGGGGC 3351.47 4673 1.394 0.332 GG GGAGGT 1639.25 2152 1.313 0.272 GG GGAGGC 3433.00 3776 1.100 0.095 GG GGCGGC 4654.67 4787 1.028 0.028 GG GGGGGT 1600.32 1543 0.964 −0.036 GG GGAGGG 2471.84 2351 0.951 −0.050 GG GGGGGA 2471.84 1517 0.614 −0.488 GG GGCGGG 3351.47 2001 0.597 −0.516 GG GGGGGG 2413.14 1080 0.448 −0.804 GG GGCGGT 2222.59 936 0.421 −0.865 GG GGCGGA 3433.00 845 0.246 −1.402 GH GGCCAC 2540.15 3679 1.448 0.370 GH GGTCAT 879.57 1022 1.162 0.150 GH GGACAT 1358.57 1438 1.058 0.057 GH GGCCAT 1842.04 1679 0.911 −0.093 GH GGGCAC 1828.97 1629 0.891 −0.116 GH GGTCAC 1212.92 1008 0.831 −0.185 GH GGACAC 1873.46 1479 0.789 −0.236 GH GGGCAT 1326.31 928 0.700 −0.357 GI GGCATC 3372.48 5474 1.623 0.484 GI GGAATA 904.63 1338 1.479 0.391 GI GGAATT 1966.96 2560 1.302 0.264 GI GGCATT 2666.92 2670 1.001 0.001 GI GGTATT 1273.45 1052 0.826 −0.191 GI GGGATC 2428.27 1958 0.806 −0.215 GI GGTATA 585.67 461 0.787 −0.239 GI GGAATC 2487.34 1910 0.768 −0.264 GI GGGATA 883.14 666 0.754 −0.282 GI GGGATT 1920.24 1421 0.740 −0.301 GI GGCATA 1226.55 885 0.722 −0.326 GI GGTATC 1610.35 931 0.578 −0.548 GK GGAAAA 3199.11 4553 1.423 0.353 GK GGGAAG 4044.81 5674 1.403 0.338 GK GGGAAA 3123.14 4119 1.319 0.277 GK GGCAAG 5617.61 5712 1.017 0.017 GK GGAAAG 4143.21 3706 0.894 −0.112 GK GGCAAA 4337.55 3581 0.826 −0.192 GK GGTAAA 2071.17 1334 0.644 −0.440 GK GGTAAG 2682.40 540 0.201 −1.603 GL GGCCTC 3017.19 4559 1.511 0.413 GL GGTTTA 579.43 820 1.415 0.347 GL GGTTTG 973.39 1294 1.329 0.285 GL GGGCTG 4514.62 5878 1.302 0.264 GL GGTCTT 993.42 1258 1.266 0.236 GL GGCCTG 6270.10 7822 1.248 0.221 GL GGGCTC 2172.45 2563 1.180 0.165 GL GGATTA 894.98 991 1.107 0.102 GL GGACTT 1534.44 1613 1.051 0.050 GL GGCTTG 2038.53 2109 1.035 0.034 GL GGCCTT 2080.48 2098 1.008 0.008 GL GGACTA 827.51 799 0.966 −0.035 GL GGGCTT 1497.99 1445 0.965 −0.036 GL GGTCTC 1440.70 1365 0.947 −0.054 GL GGTCTA 535.75 487 0.909 −0.095 GL GGGCTA 807.86 726 0.899 −0.107 GL GGCCTA 1121.99 968 0.863 −0.148 GL GGCTTA 1213.47 935 0.771 −0.261 GL GGACTC 2225.29 1656 0.744 −0.295 GL GGATTG 1503.50 1062 0.706 −0.348 GL GGTCTG 2993.96 2034 0.679 −0.387 GL GGGTTG 1467.79 870 0.593 −0.523 GL GGGTTA 873.73 467 0.534 −0.626 GL GGACTG 4624.44 2384 0.516 −0.663 GM GGCATG 3177.11 3953 1.244 0.219 GM GGAATG 2343.24 2482 1.059 0.058 GM GGGATG 2287.59 2247 0.982 −0.018 GM GGTATG 1517.06 643 0.424 −0.858 GN GGAAAT 2150.19 3332 1.550 0.438 GN GGGAAC 2311.93 2816 1.218 0.197 GN GGCAAC 3210.92 3701 1.153 0.142 GN GGAAAC 2368.18 2679 1.131 0.123 GN GGGAAT 2099.13 1823 0.868 −0.141 GN GGCAAT 2915.36 2061 0.707 −0.347 GN GGTAAT 1392.08 784 0.563 −0.574 GN GGTAAC 1533.21 785 0.512 −0.669 GP GGGCCC 2634.22 3947 1.498 0.404 GP GGGCCG 954.47 1417 1.485 0.395 GP GGCCCC 3658.52 4576 1.251 0.224 GP GGCCCG 1325.61 1623 1.224 0.202 GP GGTCCT 1564.62 1910 1.221 0.199 GP GGGCCT 2359.31 2542 1.077 0.075 GP GGTCCC 1746.93 1827 1.046 0.045 GP GGCCCT 3276.71 2994 0.914 −0.090 GP GGGCCA 2277.03 2003 0.880 −0.128 GP GGTCCA 1510.06 1264 0.837 −0.178 GP GGACCC 2698.30 2240 0.830 −0.186 GP GGACCA 2332.42 1908 0.818 −0.201 GP GGACCT 2416.70 1957 0.810 −0.211 GP GGCCCA 3162.44 2548 0.806 −0.216 GP GGTCCG 632.98 351 0.555 −0.590 GP GGACCG 977.69 421 0.431 −0.843 GQ GGACAA 1382.58 1677 1.213 0.193 GQ GGGCAG 3769.06 4425 1.174 0.160 GQ GGCCAG 5234.64 6081 1.162 0.150 GQ GGTCAA 895.11 953 1.065 0.063 GQ GGCCAA 1874.58 1593 0.850 −0.163 GQ GGGCAA 1349.74 1124 0.833 −0.183 GQ GGACAG 3860.75 3134 0.812 −0.209 GQ GGTCAG 2499.53 1879 0.752 −0.285 GR GGCCGC 1832.29 3615 1.973 0.680 GR GGAAGA 1490.60 2294 1.539 0.431 GR GGCCGG 2003.98 2892 1.443 0.367 GR GGCCGT 784.47 1022 1.303 0.265 GR GGTCGT 374.58 450 1.201 0.183 GR GGCCGA 1086.32 1252 1.153 0.142 GR GGGCGC 1319.29 1471 1.115 0.109 GR GGTCGA 518.71 546 1.053 0.051 GR GGCAGG 1984.13 2022 1.019 0.019 GR GGGAGG 1428.62 1435 1.004 0.004 GR GGGCGG 1442.91 1437 0.996 −0.004 GR GGAAGG 1463.37 1370 0.936 −0.066 GR GGGAGA 1455.20 1344 0.924 −0.079 GR GGACGT 578.58 514 0.888 −0.118 GR GGACGA 801.20 671 0.837 −0.177 GR GGGCGT 564.84 471 0.834 −0.182 GR GGCAGA 2021.05 1684 0.833 −0.182 GR GGGCGA 782.17 626 0.800 −0.223 GR GGTCGC 874.92 596 0.681 −0.384 GR GGTCGG 956.90 555 0.580 −0.545 GR GGTAGA 965.05 529 0.548 −0.601 GR GGACGC 1351.39 729 0.539 −0.617 GR GGACGG 1478.01 737 0.499 −0.696 GR GGTAGG 947.42 244 0.258 −1.357 GS GGCAGC 3581.32 6542 1.827 0.603 GS GGCTCC 3161.05 5376 1.701 0.531 GS GGCTCG 835.91 1323 1.583 0.459 GS GGCAGT 2259.47 2875 1.272 0.241 GS GGAAGT 1666.45 2085 1.251 0.224 GS GGTTCT 1313.02 1563 1.190 0.174 GS GGCTCT 2749.80 3087 1.123 0.116 GS GGGAGC 2578.63 2566 0.995 −0.005 GS GGTTCC 1509.39 1428 0.946 −0.055 GS GGCTCA 2223.05 2101 0.945 −0.056 GS GGTTCA 1061.50 981 0.924 −0.079 GS GGAAGC 2641.36 2137 0.809 −0.212 GS GGATCA 1639.59 1281 0.781 −0.247 GS GGGAGT 1626.88 1267 0.779 −0.250 GS GGATCT 2028.08 1470 0.725 −0.322 GS GGGTCC 2276.03 1646 0.723 −0.324 GS GGGTCT 1979.92 1280 0.646 −0.436 GS GGGTCG 601.87 379 0.630 −0.463 GS GGTAGT 1078.89 646 0.599 −0.513 GS GGATCC 2331.40 1342 0.576 −0.552 GS GGGTCA 1600.65 887 0.554 −0.590 GS GGTTCG 399.14 209 0.524 −0.647 GS GGATCG 616.51 276 0.448 −0.804 GS GGTAGC 1710.07 723 0.423 −0.861 GT GGCACC 3271.07 4870 1.489 0.398 GT GGCACG 1074.53 1368 1.273 0.241 GT GGGACC 2355.25 2817 1.196 0.179 GT GGAACA 1953.05 2290 1.173 0.159 GT GGAACT 1727.13 1900 1.100 0.095 GT GGGACG 773.69 838 1.083 0.080 GT GGGACA 1906.66 1903 0.998 −0.002 GT GGCACT 2341.75 2331 0.995 −0.005 GT GGCACA 2648.06 2499 0.944 −0.058 GT GGGACT 1686.11 1534 0.910 −0.095 GT GGAACC 2412.54 1841 0.763 −0.270 GT GGTACT 1118.18 840 0.751 −0.286 GT GGTACC 1561.93 994 0.636 −0.452 GT GGTACA 1264.44 780 0.617 −0.483 GT GGAACG 792.51 445 0.562 −0.577 GT GGTACG 513.09 150 0.292 −1.230 GV GGTGTT 816.93 1802 2.206 0.791 GV GGTGTC 1045.94 2070 1.979 0.683 GV GGTGTA 530.46 957 1.804 0.590 GV GGTGTG 2069.18 3207 1.550 0.438 GV GGAGTA 819.35 1225 1.495 0.402 GV GGAGTT 1261.83 1841 1.459 0.378 GV GGGGTC 1577.18 2150 1.363 0.310 GV GGAGTC 1615.55 1839 1.138 0.130 GV GGGGTT 1231.86 1123 0.912 −0.093 GV GGGGTG 3120.14 2770 0.888 −0.119 GV GGAGTG 3196.04 2641 0.826 −0.191 GV GGGGTA 799.89 631 0.789 −0.237 GV GGCGTC 2190.46 1653 0.755 −0.282 GV GGCGTG 4333.39 2790 0.644 −0.440 GV GGCGTT 1710.87 499 0.292 −1.232 GV GGCGTA 1110.93 232 0.209 −1.566 GW GGCTGG 2102.85 3748 1.782 0.578 GW GGTTGG 1004.11 690 0.687 −0.375 GW GGATGG 1550.94 1012 0.653 −0.427 GW GGGTGG 1514.10 722 0.477 −0.741 GY GGCTAC 2577.81 4581 1.777 0.575 GY GGTTAT 1000.20 1309 1.309 0.269 GY GGCTAT 2094.66 2528 1.207 0.188 GY GGATAT 1544.90 1478 0.957 −0.044 GY GGTTAC 1230.90 1074 0.873 −0.136 GY GGATAC 1901.24 1052 0.553 −0.592 GY GGGTAC 1856.09 982 0.529 −0.637 GY GGGTAT 1508.21 710 0.471 −0.753 HA CATGCT 1101.90 1959 1.778 0.575 HA CATGCA 964.61 1670 1.731 0.549 HA CATGCC 1675.52 2408 1.437 0.363 HA CACGCG 624.72 681 1.090 0.086 HA CATGCG 453.03 447 0.987 −0.013 HA CACGCC 2310.52 1649 0.714 −0.337 HA CACGCA 1330.18 617 0.464 −0.768 HA CACGCT 1519.52 549 0.361 −1.018 HC CACTGC 1778.65 2629 1.478 0.391 HC CACTGT 1498.13 1717 1.146 0.136 HC CATTGT 1086.40 673 0.619 −0.479 HC CATTGC 1289.82 634 0.492 −0.710 HD CATGAT 1329.76 2349 1.766 0.569 HD CATGAC 1502.11 2329 1.550 0.439 HD CACGAC 2071.40 1343 0.648 −0.433 HD CACGAT 1833.73 716 0.390 −0.940 HE CATGAA 1769.46 3512 1.985 0.686 HE CATGAG 2366.33 3307 1.398 0.335 HE CACGAG 3263.15 2230 0.683 −0.381 HE CACGAA 2440.07 790 0.324 −1.128 HF CACTTC 2538.66 3116 1.227 0.205 HF CATTTT 1608.41 1806 1.123 0.116 HF CACTTT 2217.98 1884 0.849 −0.163 HF CATTTC 1840.95 1400 0.760 −0.274 HG CATGGA 1246.72 2238 1.795 0.585 HG CATGGT 807.15 1426 1.767 0.569 HG CATGGG 1217.11 1849 1.519 0.418 HG CATGGC 1690.37 2320 1.372 0.317 HG CACGGC 2331.01 1680 0.721 −0.328 HG CACGGG 1678.38 1184 0.705 −0.349 HG CACGGT 1113.05 468 0.420 −0.866 HG CACGGA 1719.21 638 0.371 −0.991 HH CACCAC 2269.33 2795 1.232 0.208 HH CATCAT 1193.37 1250 1.047 0.046 HH CACCAT 1645.65 1453 0.883 −0.125 HH CATCAC 1645.65 1256 0.763 −0.270 HI CACATC 2433.52 3538 1.454 0.374 HI CACATT 1924.40 1924 1.000 0.000 HI CACATA 885.05 867 0.980 −0.021 HI CATATT 1395.51 1260 0.903 −0.102 HI CATATA 641.81 552 0.860 −0.151 HI CATATC 1764.71 904 0.512 −0.669 HK CACAAG 3102.81 3928 1.266 0.236 HK CACAAA 2395.79 2432 1.015 0.015 HK CATAAA 1737.35 1690 0.973 −0.028 HK CATAAG 2250.06 1436 0.638 −0.449 HL CATTTA 707.71 1053 1.488 0.397 HL CATTTG 1188.90 1485 1.249 0.222 HL CACCTG 5042.69 6030 1.196 0.179 HL CACCTC 2426.56 2850 1.175 0.161 HL CATCTT 1213.36 1409 1.161 0.149 HL CACTTG 1639.48 1700 1.037 0.036 HL CATCTA 654.36 649 0.992 −0.008 HL CACCTT 1673.21 1499 0.896 −0.110 HL CACCTA 902.35 761 0.843 −0.170 HL CATCTC 1759.66 1422 0.808 −0.213 HL CACTTA 975.93 781 0.800 −0.223 HL CATCTG 3656.80 2202 0.602 −0.507 HM CACATG 2348.18 3023 1.287 0.253 HM CATATG 1702.82 1028 0.604 −0.505 HN CACAAC 2031.88 2762 1.359 0.307 HN CACAAT 1844.85 1832 0.993 −0.007 HN CATAAT 1337.83 1225 0.916 −0.088 HN CATAAC 1473.45 869 0.590 −0.528 HP CACCCG 846.94 1341 1.583 0.460 HP CATCCT 1518.15 1770 1.166 0.153 HP CACCCC 2337.46 2530 1.082 0.079 HP CATCCA 1465.21 1577 1.076 0.074 HP CACCCA 2020.51 1919 0.950 −0.052 HP CACCCT 2093.51 1859 0.888 −0.119 HP CATCCC 1695.05 1265 0.746 −0.293 HP CATCCG 614.18 330 0.537 −0.621 HQ CATCAA 1143.96 1358 1.187 0.172 HQ CACCAG 4405.09 4761 1.081 0.078 HQ CATCAG 3194.43 2957 0.926 −0.077 HQ CACCAA 1577.51 1245 0.789 −0.237 HR CACAGG 1447.19 1936 1.338 0.291 HR CACCGC 1336.44 1772 1.326 0.282 HR CACAGA 1474.12 1788 1.213 0.193 HR CACCGG 1461.67 1772 1.212 0.193 HR CACCGT 572.18 667 1.166 0.153 HR CATCGA 574.58 627 1.091 0.087 HR CATCGT 414.93 452 1.089 0.086 HR CACCGA 792.34 855 1.079 0.076 HR CATCGG 1059.96 729 0.688 −0.374 HR CATAGA 1068.98 635 0.594 −0.521 HR CATCGC 969.15 565 0.583 −0.540 HR CATAGG 1049.46 423 0.403 −0.909 HS CACTCG 551.81 880 1.595 0.467 HS CACAGC 2364.16 3726 1.576 0.455 HS CACAGT 1491.56 1957 1.312 0.272 HS CATTCA 1064.20 1307 1.228 0.206 HS CATTCT 1316.36 1517 1.152 0.142 HS CACTCC 2086.72 1964 0.941 −0.061 HS CACTCA 1467.52 1318 0.898 −0.107 HS CATTCC 1513.23 1219 0.806 −0.216 HS CACTCT 1815.24 1231 0.678 −0.388 HS CATAGT 1081.63 710 0.656 −0.421 HS CATTCG 400.16 256 0.640 −0.447 HS CATAGC 1714.41 782 0.456 −0.785 HT CACACG 778.62 1526 1.960 0.673 HT CACACT 1696.86 2036 1.200 0.182 HT CACACA 1918.82 2255 1.175 0.161 HT CACACC 2370.26 2537 1.070 0.068 HT CATACT 1230.51 1306 1.061 0.060 HT CATACA 1391.46 979 0.704 −0.352 HT CATACC 1718.84 806 0.469 −0.757 HT CATACG 564.63 225 0.398 −0.920 HV CATGTT 869.32 1563 1.798 0.587 HV CATGTA 564.48 880 1.559 0.444 HV CATGTC 1113.00 1607 1.444 0.367 HV CATGTG 2201.86 2797 1.270 0.239 HV CACGTG 3036.34 2579 0.849 −0.163 HV CACGTC 1534.82 1158 0.754 −0.282 HV CACGTT 1198.78 434 0.362 −1.016 HV CACGTA 778.41 279 0.358 −1.026 HW CACTGG 1602.74 2197 1.371 0.315 HW CATTGG 1162.26 568 0.489 −0.716 HY CACTAC 1943.40 2385 1.227 0.205 HY CATTAT 1145.15 1240 1.083 0.080 HY CACTAT 1579.16 1378 0.873 −0.136 HY CATTAC 1409.29 1074 0.762 −0.272 IA ATTGCT 1886.56 3678 1.950 0.668 IA ATAGCA 759.54 1446 1.904 0.644 IA ATTGCA 1651.49 2818 1.706 0.534 IA ATAGCT 867.65 1289 1.486 0.396 IA ATTGCC 2868.63 3435 1.197 0.180 IA ATAGCC 1319.32 1191 0.903 −0.102 IA ATCGCG 980.82 708 0.722 −0.326 IA ATCGCC 3627.56 2570 0.708 −0.345 IA ATTGCG 775.62 494 0.637 −0.451 IA ATAGCG 356.72 198 0.555 −0.589 IA ATCGCA 2088.41 831 0.398 −0.922 IA ATCGCT 2385.67 910 0.381 −0.964 IC ATCTGC 2115.05 3055 1.444 0.368 IC ATCTGT 1781.48 2074 1.164 0.152 IC ATATGT 647.91 731 1.128 0.121 IC ATTTGT 1408.77 1197 0.850 −0.163 IC ATATGC 769.23 470 0.611 −0.493 IC ATTTGC 1672.56 868 0.519 −0.656 ID ATTGAT 2604.76 4341 1.667 0.511 ID ATAGAT 1197.96 1947 1.625 0.486 ID ATTGAC 2942.37 3938 1.338 0.291 ID ATAGAC 1353.23 1476 1.091 0.087 ID ATCGAC 3720.81 2270 0.610 −0.494 ID ATCGAT 3293.87 1141 0.346 −1.060 IE ATAGAA 1371.51 2939 2.143 0.762 IE ATTGAA 2982.12 5518 1.850 0.615 IE ATTGAG 3988.04 4634 1.162 0.150 IE ATAGAG 1834.15 1898 1.035 0.034 IE ATCGAG 5043.12 3007 0.596 −0.517 IE ATCGAA 3771.07 994 0.264 −1.333 IF ATATTT 1144.73 1929 1.685 0.522 IF ATCTTC 3602.60 4836 1.342 0.294 IF ATTTTT 2489.02 2226 0.894 −0.112 IF ATCTTT 3147.52 2779 0.883 −0.125 IF ATATTC 1310.24 886 0.676 −0.391 IF ATTTTC 2848.89 1887 0.662 −0.412 IG ATTGGT 1013.16 2102 2.075 0.730 IG ATTGGA 1564.91 3151 2.014 0.700 IG ATAGGA 719.72 1054 1.464 0.381 IG ATTGGG 1527.75 2144 1.403 0.339 IG ATAGGT 465.96 596 1.279 0.246 IG ATTGGC 2121.81 2706 1.275 0.243 IG ATAGGG 702.63 549 0.781 −0.247 IG ATAGGC 975.84 700 0.717 −0.332 IG ATCGGG 1931.93 1244 0.644 −0.440 IG ATCGGC 2683.15 1619 0.603 −0.505 IG ATCGGT 1281.20 498 0.389 −0.945 IG ATCGGA 1978.93 604 0.305 −1.187 IH ATTCAT 1622.93 2242 1.381 0.323 IH ATCCAC 2830.09 3367 1.190 0.174 IH ATACAT 746.40 760 1.018 0.018 IH ATCCAT 2052.29 1814 0.884 −0.123 IH ATTCAC 2238.00 1778 0.794 −0.230 IH ATACAC 1029.28 558 0.542 −0.612 II ATCATC 3797.03 5979 1.575 0.454 II ATAATA 502.24 700 1.394 0.332 II ATAATT 1092.04 1309 1.199 0.181 II ATCATT 3002.64 3321 1.106 0.101 II ATTATT 2374.46 2157 0.908 −0.096 II ATCATA 1380.95 1183 0.857 −0.155 II ATTATA 1092.04 921 0.843 −0.170 II ATAATC 1380.95 715 0.518 −0.658 II ATTATC 3002.64 1340 0.446 −0.807 IK ATAAAA 1419.09 2244 1.581 0.458 IK ATCAAG 5053.39 5884 1.164 0.152 IK ATAAAG 1837.88 1943 1.057 0.056 IK ATTAAA 3085.58 3107 1.007 0.007 IK ATCAAA 3901.90 3830 0.982 −0.019 IK ATTAAG 3996.16 2286 0.572 −0.559 IL ATTTTA 977.08 1679 1.718 0.541 IL ATATTA 449.37 723 1.609 0.476 IL ATTTTG 1641.41 2339 1.425 0.354 IL ATTCTT 1675.18 2271 1.356 0.304 IL ATCCTC 3072.14 4017 1.308 0.268 IL ATCCTG 6384.29 7754 1.215 0.194 IL ATTCTA 903.41 1021 1.130 0.122 IL ATCTTG 2075.66 2250 1.084 0.081 IL ATCCTA 1142.42 1170 1.024 0.024 IL ATACTA 415.49 416 1.001 0.001 IL ATCCTT 2118.37 2058 0.972 −0.029 IL ATATTG 754.90 717 0.950 −0.052 IL ATACTT 770.44 726 0.942 −0.059 IL ATCTTA 1235.57 1077 0.872 −0.137 IL ATTCTC 2429.41 1918 0.789 −0.236 IL ATTCTG 5048.62 3005 0.595 −0.519 IL ATACTC 1117.32 458 0.410 −0.892 IL ATACTG 2321.92 934 0.402 −0.911 IM ATCATG 3206.80 4314 1.345 0.297 IM ATAATG 1166.29 1196 1.025 0.025 IM ATTATG 2535.90 1399 0.552 −0.595 IN ATAAAT 1088.42 1649 1.515 0.415 IN ATCAAC 3296.07 4599 1.395 0.333 IN ATCAAT 2992.68 2890 0.966 −0.035 IN ATAAAC 1198.76 1113 0.928 −0.074 IN ATTAAT 2366.58 1967 0.831 −0.185 IN ATTAAC 2606.49 1331 0.511 −0.672 IP ATTCCT 2051.78 2787 1.358 0.306 IP ATTCCA 1980.23 2644 1.335 0.289 IP ATACCA 910.73 1047 1.150 0.139 IP ATCCCC 2896.94 3229 1.115 0.109 IP ATACCT 943.64 995 1.054 0.053 IP ATCCCG 1049.66 1073 1.022 0.022 IP ATCCCA 2504.13 2366 0.945 −0.057 IP ATCCCT 2594.61 2451 0.945 −0.057 IP ATTCCC 2290.86 1775 0.775 −0.255 IP ATACCC 1053.60 610 0.579 −0.547 IP ATTCCG 830.06 386 0.465 −0.766 IP ATACCG 381.76 125 0.327 −1.116 IQ ATACAA 765.47 950 1.241 0.216 IQ ATTCAA 1664.38 2045 1.229 0.206 IQ ATCCAG 5877.26 6881 1.171 0.158 IQ ATTCAG 4647.67 3987 0.858 −0.153 IQ ATCCAA 2104.71 1765 0.839 −0.176 IQ ATACAG 2137.52 1569 0.734 −0.309 IR ATCCGC 1552.18 2623 1.690 0.525 IR ATTCGA 727.72 1142 1.569 0.451 IR ATCCGA 920.25 1434 1.558 0.444 IR ATCCGT 664.55 943 1.419 0.350 IR ATAAGA 622.67 877 1.408 0.342 IR ATCCGG 1697.63 2265 1.334 0.288 IR ATTCGT 525.51 677 1.288 0.253 IR ATCAGA 1712.09 1680 0.981 −0.019 IR ATCAGG 1680.81 1513 0.900 −0.105 IR ATAAGG 611.30 547 0.895 −0.111 IR ATACGT 241.69 213 0.881 −0.126 IR ATACGA 334.69 292 0.872 −0.136 IR ATTCGG 1342.46 907 0.676 −0.392 IR ATTAGA 1353.90 900 0.665 −0.408 IR ATTCGC 1227.45 780 0.635 −0.453 IR ATACGG 617.42 260 0.421 −0.865 IR ATTAGG 1329.16 503 0.378 −0.972 IR ATACGC 564.52 170 0.301 −1.200 IS ATCTCC 2689.59 3743 1.392 0.330 IS ATATCA 687.92 954 1.387 0.327 IS ATCAGC 3047.17 3998 1.312 0.272 IS ATTTCT 1850.19 2423 1.310 0.270 IS ATTTCA 1495.77 1957 1.308 0.269 IS ATCAGT 1922.48 2287 1.190 0.174 IS ATATCT 850.92 1012 1.189 0.173 IS ATCTCG 711.23 773 1.087 0.083 IS ATAAGT 699.19 695 0.994 −0.006 IS ATCTCT 2339.68 2317 0.990 −0.010 IS ATCTCA 1891.49 1767 0.934 −0.068 IS ATTTCC 2126.89 1795 0.844 −0.170 IS ATATCC 978.18 703 0.719 −0.330 IS ATTAGT 1520.28 906 0.596 −0.518 IS ATAAGC 1108.24 636 0.574 −0.555 IS ATATCG 258.67 132 0.510 −0.673 IS ATTTCG 562.43 255 0.453 −0.791 IS ATTAGC 2409.67 797 0.331 −1.106 IT ATCACC 3094.94 4722 1.526 0.422 IT ATCACG 1016.68 1306 1.285 0.250 IT ATAACT 805.82 1009 1.252 0.225 IT ATCACT 2215.66 2751 1.242 0.216 IT ATCACA 2505.48 2989 1.193 0.176 IT ATAACA 911.22 1079 1.184 0.169 IT ATTACT 1752.12 1369 0.781 −0.247 IT ATTACA 1981.30 1531 0.773 −0.258 IT ATAACC 1125.61 741 0.658 −0.418 IT ATAACG 369.76 204 0.552 −0.595 IT ATTACC 2447.44 1083 0.443 −0.815 IT ATTACG 803.98 246 0.306 −1.184 IV ATTGTT 1261.28 2414 1.914 0.649 IV ATTGTA 819.00 1478 1.805 0.590 IV ATAGTA 376.67 645 1.712 0.538 IV ATAGTT 580.08 877 1.512 0.413 IV ATTGTC 1614.84 2315 1.434 0.360 IV ATTGTG 3194.65 3762 1.178 0.163 IV ATCGTC 2042.07 1679 0.822 −0.196 IV ATAGTG 1469.26 1196 0.814 −0.206 IV ATAGTC 742.69 575 0.774 −0.256 IV ATCGTG 4039.83 2922 0.723 −0.324 IV ATCGTA 1035.67 361 0.349 −1.054 IV ATCGTT 1594.97 547 0.343 −1.070 IW ATCTGG 1887.23 2427 1.286 0.252 IW ATATGG 686.37 622 0.906 −0.098 IW ATTTGG 1492.40 1017 0.681 −0.384 IY ATCTAC 2708.47 3486 1.287 0.252 IY ATATAT 800.43 953 1.191 0.174 IY ATTTAT 1740.39 1984 1.140 0.131 IY ATCTAT 2200.83 2196 0.998 −0.002 IY ATTTAC 2141.83 1403 0.655 −0.423 IY ATATAC 985.05 555 0.563 −0.574 KA AAAGCA 3029.93 4322 1.426 0.355 KA AAAGCT 3461.21 4262 1.231 0.208 KA AAGGCC 6816.15 6676 0.979 −0.021 KA AAGGCG 1842.96 1790 0.971 −0.029 KA AAGGCA 3924.10 3654 0.931 −0.071 KA AAAGCC 5262.99 4742 0.901 −0.104 KA AAGGCT 4482.65 4032 0.899 −0.106 KA AAAGCG 1423.01 765 0.538 −0.621 KC AAATGT 1815.55 2671 1.471 0.386 KC AAGTGT 2351.33 2267 0.964 −0.037 KC AAGTGC 2791.62 2498 0.895 −0.111 KC AAATGC 2155.50 1678 0.778 −0.250 KD AAAGAT 4684.00 6115 1.306 0.267 KD AAGGAC 6852.58 6836 0.998 −0.002 KD AAGGAT 6066.30 5379 0.887 −0.120 KD AAAGAC 5291.12 4564 0.863 −0.148 KE AAAGAA 6989.41 9895 1.416 0.348 KE AAGGAG 12105.47 12287 1.015 0.015 KE AAGGAA 9052.06 8366 0.924 −0.079 KE AAAGAG 9347.06 6946 0.743 −0.297 KF AAATTT 2631.62 3140 1.193 0.177 KF AAGTTT 3408.25 3638 1.067 0.065 KF AAGTTC 3901.02 3950 1.013 0.012 KF AAATTC 3012.11 2225 0.739 −0.303 KG AAAGGA 2672.15 4509 1.687 0.523 KG AAAGGT 1730.00 2402 1.388 0.328 KG AAAGGC 3623.06 3435 0.948 −0.053 KG AAAGGG 2608.69 2465 0.945 −0.057 KG AAGGGC 4692.27 4309 0.918 −0.085 KG AAGGGT 2240.55 1978 0.883 −0.125 KG AAGGGG 3378.54 2740 0.811 −0.209 KG AAGGGA 3460.73 2568 0.742 −0.298 KH AAACAT 1929.29 2356 1.221 0.200 KH AAGCAC 3445.60 3583 1.040 0.039 KH AAGCAT 2498.64 2430 0.973 −0.028 KH AAACAC 2660.47 2165 0.814 −0.206 KI AAAATA 1547.96 2667 1.723 0.544 KI AAAATT 3365.76 3894 1.157 0.146 KI AAGATC 5512.26 5523 1.002 0.002 KI AAGATA 2004.77 1943 0.969 −0.031 KI AAGATT 4359.03 3732 0.856 −0.155 KI AAAATC 4256.21 3287 0.772 −0.258 KK AAGAAG 11070.03 13815 1.248 0.222 KK AAGAAA 8547.55 10129 1.185 0.170 KK AAAAAG 8547.55 6145 0.719 −0.330 KK AAAAAA 6599.86 4676 0.708 −0.345 KL AAATTA 1273.72 2084 1.636 0.492 KL AAACTA 1177.70 1750 1.486 0.396 KL AAACTT 2183.78 3014 1.380 0.322 KL AAGCTG 8523.68 9600 1.126 0.119 KL AAGCTA 1525.25 1660 1.088 0.085 KL AAGCTC 4101.62 4076 0.994 −0.006 KL AAATTG 2139.75 2113 0.987 −0.013 KL AAGCTT 2828.24 2772 0.980 −0.020 KL AAGTTA 1649.61 1459 0.884 −0.123 KL AAACTC 3167.00 2653 0.838 −0.177 KL AAGTTG 2771.21 2280 0.823 −0.195 KL AAACTG 6581.43 4462 0.678 −0.389 KM AAGATG 5479.27 5650 1.031 0.031 KM AAAATG 4230.73 4060 0.960 −0.041 KN AAAAAT 3683.47 4378 1.189 0.173 KN AAGAAC 5254.13 5515 1.050 0.048 KN AAGAAT 4770.51 4618 0.968 −0.032 KN AAAAAC 4056.89 3254 0.802 −0.221 KP AAACCA 2803.51 3370 1.202 0.184 KP AAGCCC 4200.41 4673 1.113 0.107 KP AAGCCA 3630.85 4035 1.111 0.106 KP AAACCT 2904.80 3118 1.073 0.071 KP AAGCCG 1521.96 1544 1.014 0.014 KP AAGCCT 3762.04 3396 0.903 −0.102 KP AAACCC 3243.28 2624 0.809 −0.212 KP AAACCG 1175.16 482 0.410 −0.891 KQ AAACAA 2178.87 3274 1.503 0.407 KQ AAGCAA 2821.88 3177 1.126 0.119 KQ AAGCAG 7879.90 8081 1.026 0.025 KQ AAACAG 6084.35 4433 0.729 −0.317 KR AAAAGA 2247.57 3147 1.400 0.337 KR AAGAGG 2857.67 3975 1.391 0.330 KR AAGAGA 2910.85 3511 1.206 0.187 KR AAAAGG 2206.51 2325 1.054 0.052 KR AAACGT 872.39 862 0.988 −0.012 KR AAGCGG 2886.27 2828 0.980 −0.020 KR AAGCGC 2638.99 2532 0.959 −0.041 KR AAACGA 1208.07 1087 0.900 −0.106 KR AAGCGT 1129.84 978 0.866 −0.144 KR AAGCGA 1564.59 1325 0.847 −0.166 KR AAACGG 2228.59 1178 0.529 −0.638 KR AAACGC 2037.65 1041 0.511 −0.672 KS AAATCA 1871.14 2533 1.354 0.303 KS AAAAGT 1901.80 2389 1.256 0.228 KS AAATCT 2314.50 2793 1.207 0.188 KS AAGTCA 2423.33 2566 1.059 0.057 KS AAGAGC 3903.97 4045 1.036 0.035 KS AAGAGT 2463.04 2459 0.998 −0.002 KS AAGTCG 911.22 904 0.992 −0.008 KS AAGTCC 3445.84 3100 0.900 −0.106 KS AAGTCT 2997.54 2675 0.892 −0.114 KS AAATCC 2660.65 2304 0.866 −0.144 KS AAAAGC 3014.39 2381 0.790 −0.236 KS AAATCG 703.58 462 0.657 −0.421 KT AAAACA 2831.74 3611 1.275 0.243 KT AAGACG 1488.17 1790 1.203 0.185 KT AAAACT 2504.18 2969 1.186 0.170 KT AAGACC 4530.26 4475 0.988 −0.012 KT AAGACA 3667.42 3574 0.975 −0.026 KT AAGACT 3243.20 2876 0.887 −0.120 KT AAAACC 3497.97 2854 0.816 −0.203 KT AAAACG 1149.07 763 0.664 −0.409 KV AAAGTA 1317.00 2214 1.681 0.519 KV AAAGTT 2028.22 3042 1.500 0.405 KV AAAGTC 2596.78 2642 1.017 0.017 KV AAGGTG 6653.25 6512 0.979 −0.021 KV AAGGTC 3363.11 3016 0.897 −0.109 KV AAGGTT 2626.77 2294 0.873 −0.135 KV AAAGTG 5137.21 4417 0.860 −0.151 KV AAGGTA 1705.66 1291 0.757 −0.279 KW AAGTGG 2598.56 2701 1.039 0.039 KW AAATGG 2006.44 1904 0.949 −0.052 KY AAATAT 2319.32 2982 1.286 0.251 KY AAGTAC 3696.62 3603 0.975 −0.026 KY AAATAC 2854.29 2763 0.968 −0.033 KY AAGTAT 3003.78 2526 0.841 −0.173 LA CTGGCG 2275.39 3643 1.601 0.471 LA TTGGCA 1575.16 2350 1.492 0.400 LA CTGGCC 8415.49 12456 1.480 0.392 LA TTGGCT 1799.36 2643 1.469 0.384 LA TTAGCA 937.64 1314 1.401 0.337 LA CTTGCT 1836.39 2345 1.277 0.244 LA CTAGCA 866.95 1107 1.277 0.244 LA CTTGCA 1607.57 1861 1.158 0.146 LA TTAGCT 1071.10 1239 1.157 0.146 LA CTGGCT 5534.46 6333 1.144 0.135 LA CTAGCT 990.35 1099 1.110 0.104 LA CTGGCA 4844.85 5013 1.035 0.034 LA TTGGCC 2736.04 2824 1.032 0.032 LA TTGGCG 739.77 623 0.842 −0.172 LA CTTGCC 2792.34 2201 0.788 −0.238 LA CTAGCC 1505.89 1159 0.770 −0.262 LA CTAGCG 407.16 253 0.621 −0.476 LA TTAGCC 1628.68 941 0.578 −0.549 LA CTTGCG 755.00 346 0.458 −0.780 LA TTAGCG 440.36 198 0.450 −0.799 LA CTCGCC 4049.56 1527 0.377 −0.975 LA CTCGCG 1094.93 390 0.356 −1.032 LA CTCGCT 2663.20 605 0.227 −1.482 LA CTCGCA 2331.36 429 0.184 −1.693 LC CTCTGC 1769.27 3523 1.991 0.689 LC CTCTGT 1490.23 2145 1.439 0.364 LC CTTTGT 1027.58 1155 1.124 0.117 LC TTATGT 599.35 627 1.046 0.045 LC CTGTGC 3676.77 3517 0.957 −0.044 LC TTGTGT 1006.86 856 0.850 −0.162 LC CTTTGC 1219.99 974 0.798 −0.225 LC CTGTGT 3096.89 2370 0.765 −0.268 LC CTATGT 554.17 417 0.752 −0.284 LC TTGTGC 1195.39 722 0.604 −0.504 LC TTATGC 711.58 368 0.517 −0.659 LC CTATGC 657.93 332 0.505 −0.684 LD TTGGAT 2174.51 3688 1.696 0.528 LD TTAGAT 1294.41 1977 1.527 0.424 LD CTGGAC 7555.23 10531 1.394 0.332 LD CTAGAT 1196.83 1584 1.323 0.280 LD TTGGAC 2456.35 2775 1.130 0.122 LD CTTGAT 2219.25 2463 1.110 0.104 LD CTGGAT 6688.33 6912 1.033 0.033 LD CTAGAC 1351.95 1390 1.028 0.028 LD CTTGAC 2506.90 1832 0.731 −0.314 LD TTAGAC 1462.19 969 0.663 −0.411 LD CTCGAC 3635.60 981 0.270 −1.310 LD CTCGAT 3218.44 658 0.204 −1.587 LE TTAGAA 1739.66 3085 1.773 0.573 LE CTAGAA 1608.51 2701 1.679 0.518 LE TTGGAA 2922.49 4652 1.592 0.465 LE CTGGAG 12021.09 18044 1.501 0.406 LE TTGGAG 3908.29 4774 1.222 0.200 LE CTAGAG 2151.09 2515 1.169 0.156 LE CTTGAA 2982.63 3161 1.060 0.058 LE CTGGAA 8988.96 7642 0.850 −0.162 LE TTAGAG 2326.48 1873 0.805 −0.217 LE CTTGAG 3988.72 2484 0.623 −0.474 LE CTCGAG 5784.58 1305 0.226 −1.489 LE CTCGAA 4325.51 512 0.118 −2.134 LF CTCTTC 2629.18 6495 2.470 0.904 LF TTATTT 923.85 1405 1.521 0.419 LF CTCTTT 2297.07 3446 1.500 0.406 LF CTTTTT 1583.93 1937 1.223 0.201 LF CTTTTC 1812.93 1936 1.068 0.066 LF CTATTT 854.20 876 1.026 0.025 LF TTGTTT 1551.99 1544 0.995 −0.005 LF CTGTTT 4773.59 2957 0.619 −0.479 LF CTGTTC 5463.77 3119 0.571 −0.561 LF TTATTC 1057.42 583 0.551 −0.595 LF TTGTTC 1776.38 940 0.529 −0.636 LF CTATTC 977.70 464 0.475 −0.745 LG CTTGGA 1534.14 2667 1.738 0.553 LG CTTGGT 993.23 1579 1.590 0.464 LG CTGGGC 6268.87 9794 1.562 0.446 LG CTAGGA 827.35 1087 1.314 0.273 LG CTTGGG 1497.70 1881 1.256 0.228 LG TTAGGA 894.81 1114 1.245 0.219 LG CTGGGG 4513.74 5602 1.241 0.216 LG TTGGGT 973.20 1194 1.227 0.204 LG TTGGGA 1503.20 1820 1.211 0.191 LG CTAGGT 535.64 611 1.141 0.132 LG TTAGGT 579.32 611 1.055 0.053 LG TTGGGG 1467.50 1452 0.989 −0.011 LG CTGGGT 2993.37 2947 0.985 −0.016 LG CTTGGC 2080.08 2009 0.966 −0.035 LG CTAGGG 807.70 766 0.948 −0.053 LG TTGGGC 2038.13 1786 0.876 −0.132 LG CTGGGA 4623.54 4034 0.872 −0.136 LG CTAGGC 1121.77 940 0.838 −0.177 LG TTAGGG 873.56 529 0.606 −0.502 LG CTCGGG 2172.02 1076 0.495 −0.702 LG CTCGGC 3016.60 1313 0.435 −0.832 LG TTAGGC 1213.24 507 0.418 −0.873 LG CTCGGT 1440.42 365 0.253 −1.373 LG CTCGGA 2224.86 510 0.229 −1.473 LH CTTCAT 1127.31 1980 1.756 0.563 LH TTACAT 657.52 935 1.422 0.352 LH CTACAT 607.95 741 1.219 0.198 LH CTGCAC 4685.05 5459 1.165 0.153 LH CTCCAC 2254.46 2204 0.978 −0.023 LH CTTCAC 1554.55 1490 0.958 −0.042 LH CTCCAT 1634.86 1521 0.930 −0.072 LH CTACAC 838.36 777 0.927 −0.076 LH TTGCAT 1104.58 1017 0.921 −0.083 LH TTGCAC 1523.20 1140 0.748 −0.290 LH CTGCAT 3397.45 2394 0.705 −0.350 LH TTACAC 906.71 634 0.699 −0.358 LI CTCATC 2602.42 6250 2.402 0.876 LI TTAATA 380.66 798 2.096 0.740 LI TTAATT 827.68 1290 1.559 0.444 LI CTCATT 2057.96 3117 1.515 0.415 LI CTAATA 351.96 516 1.466 0.383 LI CTAATT 765.28 952 1.244 0.218 LI CTTATT 1419.05 1761 1.241 0.216 LI TTGATA 639.48 791 1.237 0.213 LI TTGATT 1390.44 1468 1.056 0.054 LI CTTATA 652.64 683 1.047 0.045 LI CTCATA 946.48 919 0.971 −0.029 LI CTTATC 1794.48 1189 0.663 −0.412 LI TTGATC 1758.29 1135 0.646 −0.438 LI CTGATC 5408.15 3356 0.621 −0.477 LI CTGATT 4276.70 2639 0.617 −0.483 LI CTGATA 1966.91 1193 0.607 −0.500 LI TTAATC 1046.66 633 0.605 −0.503 LI CTAATC 967.75 563 0.582 −0.542 LK TTAAAA 1429.91 2557 1.788 0.581 LK CTAAAA 1322.10 1842 1.393 0.332 LK TTGAAA 2402.12 3193 1.329 0.285 LK CTCAAG 4604.55 6048 1.313 0.273 LK CTAAAG 1712.27 2078 1.214 0.194 LK TTAAAG 1851.89 2128 1.149 0.139 LK CTGAAG 9568.82 10212 1.067 0.065 LK TTGAAG 3111.01 3222 1.036 0.035 LK CTCAAA 3555.33 2768 0.779 −0.250 LK CTTAAA 2451.55 1850 0.755 −0.282 LK CTGAAA 7388.42 5227 0.707 −0.346 LK CTTAAG 3175.03 1448 0.456 −0.785 LL TTATTA 500.55 802 1.602 0.471 LL CTTCTA 793.49 1132 1.427 0.355 LL CTTCTT 1471.36 2099 1.427 0.355 LL CTTTTA 858.19 1203 1.402 0.338 LL CTGCTG 13364.10 18236 1.365 0.311 LL CTTTTG 1441.69 1945 1.349 0.299 LL TTACTA 462.82 608 1.314 0.273 LL CTCCTC 3094.54 3800 1.228 0.205 LL CTCCTG 6430.85 7786 1.211 0.191 LL TTACTT 858.19 1039 1.211 0.191 LL TTGCTA 777.49 929 1.195 0.178 LL CTGCTC 6430.85 7550 1.174 0.160 LL CTACTA 427.93 474 1.108 0.102 LL CTTCTC 2133.82 2292 1.074 0.072 LL CTACTT 793.49 839 1.057 0.056 LL CTCTTG 2090.79 2131 1.019 0.019 LL TTGCTT 1441.69 1464 1.015 0.015 LL TTATTG 840.89 818 0.973 −0.028 LL CTCCTT 2133.82 2034 0.953 −0.048 LL TTGTTA 840.89 771 0.917 −0.087 LL TTGTTG 1412.62 1289 0.912 −0.092 LL CTCCTA 1150.75 1034 0.899 −0.107 LL TTGCTG 4344.93 3820 0.879 −0.129 LL CTTCTG 4434.34 3837 0.865 −0.145 LL CTGCTA 2391.41 1913 0.800 −0.223 LL CTCTTA 1244.58 959 0.771 −0.261 LL CTATTA 462.82 354 0.765 −0.268 LL CTGCTT 4434.34 3148 0.710 −0.343 LL TTGCTC 2090.79 1440 0.689 −0.373 LL CTACTC 1150.75 792 0.688 −0.374 LL CTATTG 777.49 532 0.684 −0.379 LL CTACTG 2391.41 1583 0.662 −0.413 LL CTGTTG 4344.93 2615 0.602 −0.508 LL TTACTC 1244.58 657 0.528 −0.639 LL TTACTG 2586.40 1358 0.525 −0.644 LL CTGTTA 2586.40 953 0.368 −0.998 LM CTCATG 2631.41 4030 1.531 0.426 LM TTAATG 1058.32 1228 1.160 0.149 LM CTAATG 978.53 1101 1.125 0.118 LM TTGATG 1777.88 1763 0.992 −0.008 LM CTGATG 5468.39 4470 0.817 −0.202 LM CTTATG 1814.47 1137 0.627 −0.467 LN TTAAAT 962.36 1926 2.001 0.694 LN CTCAAC 2635.40 4681 1.776 0.574 LN CTAAAT 889.81 1446 1.625 0.486 LN TTGAAT 1616.68 2048 1.267 0.236 LN CTCAAT 2392.82 2652 1.108 0.103 LN CTAAAC 980.01 922 0.941 −0.061 LN TTAAAC 1059.92 965 0.910 −0.094 LN CTTAAT 1649.95 1441 0.873 −0.135 LN TTGAAC 1780.58 1541 0.865 −0.145 LN CTGAAC 5476.68 4308 0.787 −0.240 LN CTGAAT 4972.58 3413 0.686 −0.376 LN CTTAAC 1817.22 891 0.490 −0.713 LP CTTCCT 1728.14 2795 1.617 0.481 LP CTTCCA 1667.88 2369 1.420 0.351 LP CTGCCC 5815.10 7856 1.351 0.301 LP TTACCT 1007.96 1244 1.234 0.210 LP CTGCCG 2107.02 2489 1.181 0.167 LP TTACCA 972.81 1140 1.172 0.159 LP CTCCCG 1013.90 1184 1.168 0.155 LP TTGCCA 1634.25 1897 1.161 0.149 LP CTACCT 931.97 1045 1.121 0.114 LP TTGCCT 1693.30 1800 1.063 0.061 LP CTTCCC 1929.51 1889 0.979 −0.021 LP CTACCA 899.47 850 0.945 −0.057 LP CTCCCA 2418.82 2126 0.879 −0.129 LP CTGCCT 5208.23 4563 0.876 −0.132 LP CTCCCT 2506.21 2192 0.875 −0.134 LP CTACCC 1040.57 888 0.853 −0.159 LP CTCCCC 2798.25 2369 0.847 −0.167 LP TTGCCC 1890.60 1560 0.825 −0.192 LP TTGCCG 685.03 478 0.698 −0.360 LP CTGCCA 5026.60 3348 0.666 −0.406 LP CTTCCG 699.13 451 0.645 −0.438 LP TTACCC 1125.42 666 0.592 −0.525 LP CTACCG 377.04 211 0.560 −0.580 LP TTACCG 407.78 175 0.429 −0.846 LQ TTACAA 864.28 1290 1.493 0.401 LQ CTACAA 799.12 1188 1.487 0.397 LQ CTTCAA 1481.79 2098 1.416 0.348 LQ CTACAG 2231.48 2674 1.198 0.181 LQ CTGCAG 12470.36 14508 1.163 0.151 LQ CTTCAG 4137.79 4363 1.054 0.053 LQ TTGCAA 1451.91 1467 1.010 0.010 LQ CTCCAG 6000.78 5430 0.905 −0.100 LQ TTACAG 2413.43 2107 0.873 −0.136 LQ TTGCAG 4054.36 3177 0.784 −0.244 LQ CTCCAA 2148.94 1524 0.709 −0.344 LQ CTGCAA 4465.77 2694 0.603 −0.505 LR CTTCGA 661.43 1365 2.064 0.725 LR CTTCGT 477.64 784 1.641 0.496 LR CTGCGG 3677.31 5467 1.487 0.397 LR TTAAGA 717.74 1026 1.429 0.357 LR CTGCGC 3362.26 4574 1.360 0.308 LR CTCCGA 959.23 1289 1.344 0.295 LR CTCCGG 1769.53 2229 1.260 0.231 LR CTAAGA 663.63 821 1.237 0.213 LR CTCAGG 1752.00 2047 1.168 0.156 LR CTTCGG 1220.17 1415 1.160 0.148 LR CTCCGT 692.69 771 1.113 0.107 LR TTACGA 385.79 427 1.107 0.101 LR CTAAGG 651.51 721 1.107 0.101 LR CTCCGC 1617.93 1790 1.106 0.101 LR TTGAGA 1205.75 1290 1.070 0.068 LR CTACGT 257.59 275 1.068 0.065 LR CTACGA 356.70 378 1.060 0.058 LR CTGAGG 3640.88 3637 0.999 −0.001 LR TTAAGG 704.63 678 0.962 −0.039 LR TTACGT 278.59 264 0.948 −0.054 LR CTGCGT 1439.50 1363 0.947 −0.055 LR TTGAGG 1183.72 1080 0.912 −0.092 LR CTACGG 658.03 577 0.877 −0.131 LR CTCAGA 1784.60 1469 0.823 −0.195 LR CTTCGC 1115.63 819 0.734 −0.309 LR CTACGC 601.65 438 0.728 −0.317 LR CTGCGA 1993.40 1399 0.702 −0.354 LR TTGCGT 468.01 321 0.686 −0.377 LR CTGAGA 3708.63 2486 0.670 −0.400 LR TTGCGG 1195.56 772 0.646 −0.437 LR TTGCGA 648.09 418 0.645 −0.439 LR CTTAGA 1230.56 694 0.564 −0.573 LR TTACGG 711.68 383 0.538 −0.620 LR TTGCGC 1093.14 542 0.496 −0.702 LR CTTAGG 1208.08 503 0.416 −0.876 LR TTACGC 650.71 232 0.357 −1.031 LS CTCAGC 2740.30 5167 1.886 0.634 LS CTTTCT 1450.83 2502 1.725 0.545 LS CTCTCC 2418.72 4070 1.683 0.520 LS CTCTCG 639.61 1016 1.588 0.463 LS CTCAGT 1728.87 2589 1.498 0.404 LS TTATCA 684.12 963 1.408 0.342 LS TTATCT 846.22 1175 1.389 0.328 LS CTTTCA 1172.91 1626 1.386 0.327 LS TTAAGT 695.33 886 1.274 0.242 LS CTCTCT 2104.05 2553 1.213 0.193 LS CTAAGT 642.91 770 1.198 0.180 LS CTCTCA 1701.00 2003 1.178 0.163 LS CTTTCC 1667.81 1819 1.091 0.087 LS TTGTCA 1149.26 1210 1.053 0.052 LS CTGTCG 1329.18 1392 1.047 0.046 LS TTGTCT 1421.58 1461 1.028 0.027 LS CTGAGC 5694.68 5805 1.019 0.019 LS CTGTCC 5026.41 4628 0.921 −0.083 LS TTGAGT 1168.09 1035 0.886 −0.121 LS TTGTCC 1634.18 1334 0.816 −0.203 LS CTATCA 632.54 512 0.809 −0.211 LS CTAAGC 1019.02 791 0.776 −0.253 LS TTATCC 972.78 727 0.747 −0.291 LS CTGAGT 3592.81 2665 0.742 −0.299 LS CTTAGT 1192.13 856 0.718 −0.331 LS CTATCT 782.42 557 0.712 −0.340 LS CTGTCT 4372.48 2950 0.675 −0.394 LS CTTTCG 441.04 291 0.660 −0.416 LS TTGTCG 432.14 278 0.643 −0.441 LS CTGTCA 3534.89 2228 0.630 −0.462 LS TTGAGC 1851.45 1128 0.609 −0.496 LS CTATCC 899.44 541 0.601 −0.508 LS TTATCG 257.24 152 0.591 −0.526 LS TTAAGC 1102.11 551 0.500 −0.693 LS CTATCG 237.85 102 0.429 −0.847 LS CTTAGC 1889.55 793 0.420 −0.868 LT CTCACC 2534.19 4959 1.957 0.671 LT CTCACG 832.47 1510 1.814 0.595 LT TTAACA 825.09 1163 1.410 0.343 LT CTCACT 1814.22 2521 1.390 0.329 LT TTAACT 729.65 969 1.328 0.284 LT CTAACT 674.64 817 1.211 0.191 LT CTAACA 762.89 898 1.177 0.163 LT CTCACA 2051.52 2374 1.157 0.146 LT CTGACG 1729.98 1795 1.038 0.037 LT TTGACT 1225.76 1259 1.027 0.027 LT TTGACA 1386.09 1401 1.011 0.011 LT CTTACT 1250.98 1259 1.006 0.006 LT CTGACC 5266.36 5160 0.980 −0.020 LT CTTACA 1414.61 1109 0.784 −0.243 LT CTGACT 3770.17 2808 0.745 −0.295 LT TTGACC 1712.20 1235 0.721 −0.327 LT CTAACC 942.38 678 0.719 −0.329 LT TTGACG 562.45 399 0.709 −0.343 LT CTGACA 4263.32 3003 0.704 −0.350 LT CTAACG 309.57 215 0.695 −0.365 LT TTAACC 1019.22 687 0.674 −0.394 LT CTTACC 1747.43 1104 0.632 −0.459 LT TTAACG 334.81 164 0.490 −0.714 LT CTTACG 574.02 247 0.430 −0.843 LV CTTGTT 1029.60 1741 1.691 0.525 LV TTAGTA 389.95 602 1.544 0.434 LV TTGGTA 655.07 980 1.496 0.403 LV CTTGTA 668.56 993 1.485 0.396 LV CTGGTG 7859.41 11424 1.454 0.374 LV CTAGTA 360.55 519 1.439 0.364 LV TTGGTT 1008.84 1427 1.414 0.347 LV CTTGTC 1318.22 1541 1.169 0.156 LV TTAGTT 600.53 690 1.149 0.139 LV CTGGTC 3972.81 4541 1.143 0.134 LV TTGGTG 2555.25 2882 1.128 0.120 LV CTAGTT 555.26 580 1.045 0.044 LV TTGGTC 1291.64 1345 1.041 0.040 LV CTTGTG 2607.83 2540 0.974 −0.026 LV CTAGTG 1406.38 1272 0.904 −0.100 LV CTGGTA 2014.87 1720 0.854 −0.158 LV CTGGTT 3102.98 2576 0.830 −0.186 LV CTAGTC 710.90 551 0.775 −0.255 LV TTAGTG 1521.06 947 0.623 −0.474 LV TTAGTC 768.87 416 0.541 −0.614 LV CTCGTC 1911.73 1013 0.530 −0.635 LV CTCGTG 3781.97 1691 0.447 −0.805 LV CTCGTT 1493.16 373 0.250 −1.387 LV CTCGTA 969.56 191 0.197 −1.625 LW CTCTGG 1742.64 2796 1.604 0.473 LW CTGTGG 3621.43 3365 0.929 −0.073 LW CTTTGG 1201.63 1018 0.847 −0.166 LW CTATGG 648.03 501 0.773 −0.257 LW TTATGG 700.87 535 0.763 −0.270 LW TTGTGG 1177.40 877 0.745 −0.295 LY CTCTAC 2082.09 4204 2.019 0.703 LY TTATAT 680.44 1022 1.502 0.407 LY CTCTAT 1691.85 2487 1.470 0.385 LY CTTTAT 1166.60 1591 1.364 0.310 LY CTATAT 629.14 596 0.947 −0.054 LY TTGTAT 1143.08 1063 0.930 −0.073 LY CTGTAC 4326.84 3390 0.783 −0.244 LY CTTTAC 1435.69 1069 0.745 −0.295 LY TTGTAC 1406.74 1006 0.715 −0.335 LY TTATAC 837.39 579 0.691 −0.369 LY CTGTAT 3515.88 2202 0.626 −0.468 LY CTATAC 774.26 481 0.621 −0.476 MA ATGGCG 1645.46 2370 1.440 0.365 MA ATGGCA 3503.58 3580 1.022 0.022 MA ATGGCT 4002.27 4003 1.000 0.000 MA ATGGCC 6085.70 5284 0.868 −0.141 MC ATGTGT 1386.67 1448 1.044 0.043 MC ATGTGC 1646.33 1585 0.963 −0.038 MD ATGGAT 4467.48 4634 1.037 0.037 MD ATGGAC 5046.52 4880 0.967 −0.034 ME ATGGAG 8054.28 8223 1.021 0.021 ME ATGGAA 6022.72 5854 0.972 −0.028 MF ATGTTT 2565.53 2833 1.104 0.099 MF ATGTTC 2936.47 2669 0.909 −0.096 MG ATGGGC 3467.73 3533 1.019 0.019 MG ATGGGT 1655.83 1675 1.012 0.012 MG ATGGGA 2557.59 2526 0.988 −0.012 MG ATGGGG 2496.85 2444 0.979 −0.021 MH ATGCAT 1465.33 1478 1.009 0.009 MH ATGCAC 2020.67 2008 0.994 −0.006 MI ATGATT 2305.40 2382 1.033 0.033 MI ATGATA 1060.28 1094 1.032 0.031 MI ATGATC 2915.32 2805 0.962 −0.039 MK ATGAAG 6107.32 6423 1.052 0.050 MK ATGAAA 4715.68 4400 0.933 −0.069 ML ATGCTG 5938.40 6536 1.101 0.096 ML ATGCTA 1062.63 1122 1.056 0.054 ML ATGTTG 1930.69 1922 0.995 −0.005 ML ATGTTA 1149.28 1134 0.987 −0.013 ML ATGCTT 1970.42 1887 0.958 −0.043 ML ATGCTC 2857.58 2308 0.808 −0.214 MM ATGATG 3925.00 3925 1.000 0.000 MN ATGAAT 3249.30 3301 1.016 0.016 MN ATGAAC 3578.70 3527 0.986 −0.015 MP ATGCCC 2676.16 2752 1.028 0.028 MP ATGCCA 2313.29 2313 1.000 0.000 MP ATGCCT 2396.87 2372 0.990 −0.010 MP ATGCCG 969.67 919 0.948 −0.054 MQ ATGCAG 5141.70 5165 1.005 0.005 MQ ATGCAA 1841.30 1818 0.987 −0.013 MR ATGAGG 1626.37 2127 1.308 0.268 MR ATGAGA 1656.63 1974 1.192 0.175 MR ATGCGG 1642.64 1513 0.921 −0.082 MR ATGCGT 643.02 531 0.826 −0.191 MR ATGCGA 890.44 684 0.768 −0.264 MR ATGCGC 1501.91 1132 0.754 −0.283 MS ATGTCG 666.33 809 1.214 0.194 MS ATGTCT 2191.95 2338 1.067 0.065 MS ATGTCA 1772.07 1781 1.005 0.005 MS ATGTCC 2519.77 2493 0.989 −0.011 MS ATGAGT 1801.10 1770 0.983 −0.017 MS ATGAGC 2854.78 2615 0.916 −0.088 MT ATGACT 2098.83 2195 1.046 0.045 MT ATGACC 2931.75 2927 0.998 −0.002 MT ATGACA 2373.36 2337 0.985 −0.015 MT ATGACG 963.07 908 0.943 −0.059 MV ATGGTG 4813.46 5122 1.064 0.062 MV ATGGTT 1900.41 1915 1.008 0.008 MV ATGGTA 1234.00 1191 0.965 −0.035 MV ATGGTC 2433.13 2153 0.885 −0.122 MW ATGTGG 1876.00 1876 1.000 0.000 MY ATGTAC 2354.66 2363 1.004 0.004 MY ATGTAT 1913.34 1905 0.996 −0.004 NA AATGCA 1705.68 3344 1.961 0.673 NA AATGCT 1948.47 3458 1.775 0.574 NA AATGCC 2962.77 4259 1.438 0.363 NA AATGCG 801.08 624 0.779 −0.250 NA AACGCG 882.29 661 0.749 −0.289 NA AACGCC 3263.12 1899 0.582 −0.541 NA AACGCA 1878.60 700 0.373 −0.987 NA AACGCT 2146.00 643 0.300 −1.205 NC AACTGC 1868.57 2826 1.512 0.414 NC AACTGT 1573.86 2016 1.281 0.248 NC AATTGT 1429.00 935 0.654 −0.424 NC AATTGC 1696.57 791 0.466 −0.763 ND AATGAT 2555.01 4420 1.730 0.548 ND AATGAC 2886.18 4521 1.566 0.449 ND AACGAC 3178.77 1654 0.520 −0.653 ND AACGAT 2814.03 839 0.298 −1.210 NE AATGAA 3381.19 7367 2.179 0.779 NE AATGAG 4521.72 5796 1.282 0.248 NE AACGAG 4980.12 2476 0.497 −0.699 NE AACGAA 3723.97 968 0.260 −1.347 NF AACTTC 3150.86 4259 1.352 0.301 NF AACTTT 2752.85 2846 1.034 0.033 NF AATTTT 2499.46 2350 0.940 −0.062 NF AATTTC 2860.84 1809 0.632 −0.458 NG AATGGA 2235.93 4484 2.005 0.696 NG AATGGT 1447.59 2430 1.679 0.518 NG AATGGG 2182.83 3202 1.467 0.383 NG AATGGC 3031.62 4001 1.320 0.277 NG AACGGG 2404.12 1508 0.627 −0.466 NG AACGGC 3338.95 1752 0.525 −0.645 NG AACGGA 2462.61 804 0.326 −1.119 NG AACGGT 1594.34 517 0.324 −1.126 NH AACCAC 2167.68 2776 1.281 0.247 NH AACCAT 1571.93 1639 1.043 0.042 NH AATCAT 1427.24 1456 1.020 0.020 NH AATCAC 1968.15 1264 0.642 −0.443 NI AACATC 3876.27 5487 1.416 0.348 NI AACATT 3065.31 3184 1.039 0.038 NI AATATA 1280.01 1309 1.023 0.022 NI AACATA 1409.77 1384 0.982 −0.018 NI AATATT 2783.16 2725 0.979 −0.021 NI AATATC 3519.48 1845 0.524 −0.646 NK AACAAG 4824.98 5918 1.227 0.204 NK AACAAA 3725.54 4221 1.133 0.125 NK AATAAA 3382.62 3607 1.066 0.064 NK AATAAG 4380.86 2568 0.586 −0.534 NL AATTTA 1025.31 1571 1.532 0.427 NL AACCTC 2807.78 3954 1.408 0.342 NL AACTTG 1897.05 2429 1.280 0.247 NL AACCTG 5834.92 6690 1.147 0.137 NL AATTTG 1722.43 1947 1.130 0.123 NL AATCTT 1757.88 1943 1.105 0.100 NL AACCTA 1044.12 1135 1.087 0.083 NL AACCTT 1936.08 2021 1.044 0.043 NL AACTTA 1129.25 1129 1.000 0.000 NL AATCTA 948.01 893 0.942 −0.060 NL AATCTC 2549.34 1713 0.672 −0.398 NL AATCTG 5297.84 2525 0.477 −0.741 NM AACATG 3351.76 4374 1.305 0.266 NM AATATG 3043.24 2021 0.664 −0.409 NN AACAAC 3150.02 4430 1.406 0.341 NN AACAAT 2860.08 2830 0.989 −0.011 NN AATAAT 2596.82 2424 0.933 −0.069 NN AATAAC 2860.08 1783 0.623 −0.473 NP AACCCC 2770.02 3474 1.254 0.226 NP AATCCA 2174.02 2380 1.095 0.091 NP AACCCA 2394.42 2612 1.091 0.087 NP AATCCT 2252.58 2414 1.072 0.069 NP AACCCG 1003.68 1048 1.044 0.043 NP AACCCT 2480.94 2578 1.039 0.038 NP AATCCC 2515.05 1641 0.652 −0.427 NP AATCCG 911.29 355 0.390 −0.943 NQ AATCAA 1516.57 1905 1.256 0.228 NQ AACCAA 1670.31 1955 1.170 0.157 NQ AACCAG 4664.22 5409 1.160 0.148 NQ AATCAG 4234.90 2817 0.665 −0.408 NR AACAGA 1511.98 2383 1.576 0.455 NR AACCGC 1370.77 1966 1.434 0.361 NR AACAGG 1484.36 1903 1.282 0.248 NR AACCGA 812.69 998 1.228 0.205 NR AACCGT 586.88 706 1.203 0.185 NR AACCGG 1499.21 1779 1.187 0.171 NR AATCGA 737.89 687 0.931 −0.071 NR AATCGT 532.86 486 0.912 −0.092 NR AATAGA 1372.81 1117 0.814 −0.206 NR AATCGC 1244.60 602 0.484 −0.726 NR AATAGG 1347.73 643 0.477 −0.740 NR AATCGG 1361.22 593 0.436 −0.831 NS AACAGC 2917.73 4490 1.539 0.431 NS AACAGT 1840.81 2414 1.311 0.271 NS AACTCG 681.02 821 1.206 0.187 NS AATTCA 1644.43 1970 1.198 0.181 NS AATTCT 2034.08 2383 1.172 0.158 NS AACTCC 2575.33 2818 1.094 0.090 NS AACTCA 1811.14 1783 0.984 −0.016 NS AACTCT 2240.29 1981 0.884 −0.123 NS AATAGT 1671.38 1193 0.714 −0.337 NS AATTCC 2338.29 1655 0.708 −0.346 NS AATAGC 2649.17 1273 0.481 −0.733 NS AATTCG 618.33 241 0.390 −0.942 NT AACACG 860.22 1238 1.439 0.364 NT AACACA 2119.90 2783 1.313 0.272 NT AACACC 2618.65 3278 1.252 0.225 NT AACACT 1874.68 2099 1.120 0.113 NT AATACT 1702.13 1540 0.905 −0.100 NT AATACA 1924.77 1692 0.879 −0.129 NT AATACC 2377.62 1312 0.552 −0.595 NT AATACG 781.04 317 0.406 −0.902 NV AATGTA 927.15 1710 1.844 0.612 NV AATGTT 1427.85 2573 1.802 0.589 NV AATGTC 1828.10 2877 1.574 0.453 NV AATGTG 3616.54 4314 1.193 0.176 NV AACGTG 3983.18 2772 0.696 −0.363 NV AACGTC 2013.43 1341 0.666 −0.406 NV AACGTT 1572.60 509 0.324 −1.128 NV AACGTA 1021.14 294 0.288 −1.245 NW AACTGG 1808.22 2595 1.435 0.361 NW AATTGG 1641.78 855 0.521 −0.652 NY AACTAC 2506.72 3191 1.273 0.241 NY AACTAT 2036.89 2145 1.053 0.052 NY AATTAT 1849.41 1795 0.971 −0.030 NY AATTAC 2275.98 1538 0.676 −0.392 PA CCGGCG 470.57 1166 2.478 0.907 PA CCGGCC 1740.39 2666 1.532 0.426 PA CCAGCA 2390.31 3368 1.409 0.343 PA CCAGCT 2730.54 3622 1.326 0.283 PA CCTGCT 2829.20 3750 1.325 0.282 PA CCTGCA 2476.67 3178 1.283 0.249 PA CCAGCC 4151.96 4942 1.190 0.174 PA CCCGCG 1298.71 1528 1.177 0.163 PA CCTGCC 4301.98 5000 1.162 0.150 PA CCAGCG 1122.61 1078 0.960 −0.041 PA CCTGCG 1163.17 1105 0.950 −0.051 PA CCGGCT 1144.57 1013 0.885 −0.122 PA CCGGCA 1001.95 777 0.775 −0.254 PA CCCGCC 4803.25 2690 0.560 −0.580 PA CCCGCA 2765.26 846 0.306 −1.184 PA CCCGCT 3158.86 821 0.260 −1.347 PC CCCTGC 1550.51 2870 1.851 0.616 PC CCCTGT 1305.97 1577 1.208 0.189 PC CCGTGC 561.80 630 1.121 0.115 PC CCTTGT 1169.67 1001 0.856 −0.156 PC CCATGT 1128.89 831 0.736 −0.306 PC CCGTGT 473.20 340 0.719 −0.331 PC CCTTGC 1388.69 937 0.675 −0.393 PC CCATGC 1340.27 733 0.547 −0.603 PD CCAGAT 2721.60 4165 1.530 0.425 PD CCTGAT 2819.94 3781 1.341 0.293 PD CCGGAC 1288.69 1659 1.287 0.253 PD CCAGAC 3074.36 3766 1.225 0.203 PD CCTGAC 3185.44 3646 1.145 0.135 PD CCGGAT 1140.82 895 0.785 −0.243 PD CCCGAC 3556.62 2215 0.623 −0.474 PD CCCGAT 3148.53 809 0.257 −1.359 PE CCAGAA 3999.86 5699 1.425 0.354 PE CCTGAG 5542.36 7122 1.285 0.251 PE CCGGAG 2242.20 2870 1.280 0.247 PE CCAGAG 5349.08 6777 1.267 0.237 PE CCTGAA 4144.39 5108 1.233 0.209 PE CCCGAG 6188.17 4149 0.670 −0.400 PE CCGGAA 1676.64 1032 0.616 −0.485 PE CCCGAA 4627.30 1013 0.219 −1.519 PF CCCTTC 2555.92 4301 1.683 0.520 PF CCATTT 1930.27 2057 1.066 0.064 PF CCTTTT 2000.01 1967 0.983 −0.017 PF CCCTTT 2233.06 2159 0.967 −0.034 PF CCTTTC 2289.18 2078 0.908 −0.097 PF CCGTTC 926.10 662 0.715 −0.336 PF CCATTC 2209.35 1290 0.584 −0.538 PF CCGTTT 809.12 439 0.543 −0.611 PG CCTGGG 2918.52 4310 1.477 0.390 PG CCTGGA 2989.52 4317 1.444 0.367 PG CCGGGC 1639.82 2353 1.435 0.361 PG CCGGGG 1180.71 1657 1.403 0.339 PG CCTGGT 1935.48 2673 1.381 0.323 PG CCAGGA 2885.27 3897 1.351 0.301 PG CCAGGG 2816.75 3472 1.233 0.209 PG CCAGGT 1867.98 2259 1.209 0.190 PG CCTGGC 4053.37 4622 1.140 0.131 PG CCAGGC 3912.02 4106 1.050 0.048 PG CCGGGT 783.01 661 0.844 −0.169 PG CCGGGA 1209.43 963 0.796 −0.228 PG CCCGGG 3258.60 2136 0.655 −0.422 PG CCCGGC 4525.68 2555 0.565 −0.572 PG CCCGGA 3337.86 968 0.290 −1.238 PG CCCGGT 2161.00 526 0.243 −1.413 PH CCGCAC 725.13 972 1.340 0.293 PH CCCCAC 2001.25 2505 1.252 0.225 PH CCTCAT 1299.79 1592 1.225 0.203 PH CCACAT 1254.46 1222 0.974 −0.026 PH CCCCAT 1451.24 1303 0.898 −0.108 PH CCTCAC 1792.40 1531 0.854 −0.158 PH CCACAC 1729.89 1366 0.790 −0.236 PH CCGCAT 525.84 289 0.550 −0.599 PI CCCATC 2119.04 4651 2.195 0.786 PI CCCATT 1675.71 2102 1.254 0.227 PI CCAATA 666.18 819 1.229 0.207 PI CCCATA 770.68 776 1.007 0.007 PI CCAATT 1448.49 1386 0.957 −0.044 PI CCTATA 690.25 603 0.874 −0.135 PI CCTATT 1500.83 1266 0.844 −0.170 PI CCAATC 1831.71 939 0.513 −0.668 PI CCTATC 1897.89 957 0.504 −0.685 PI CCGATT 607.17 299 0.492 −0.708 PI CCGATC 767.80 342 0.445 −0.809 PI CCGATA 279.24 115 0.412 −0.887 PK CCCAAG 3738.47 6383 1.707 0.535 PK CCCAAA 2886.60 3787 1.312 0.271 PK CCAAAA 2495.20 2489 0.998 −0.002 PK CCAAAG 3231.55 3127 0.968 −0.033 PK CCTAAA 2585.35 1840 0.712 −0.340 PK CCGAAG 1354.58 940 0.694 −0.365 PK CCTAAG 3348.32 1660 0.496 −0.702 PK CCGAAA 1045.92 460 0.440 −0.821 PL CCGCTG 1824.84 3343 1.832 0.605 PL CCGCTC 878.12 1254 1.428 0.356 PL CCTTTG 1466.52 2054 1.401 0.337 PL CCTTTA 872.97 1195 1.369 0.314 PL CCCTTG 1637.40 2122 1.296 0.259 PL CCTCTT 1496.70 1827 1.221 0.199 PL CCCCTG 5036.31 5760 1.144 0.134 PL CCCCTC 2423.49 2646 1.092 0.088 PL CCTCTA 807.16 871 1.079 0.076 PL CCATTA 842.53 826 0.980 −0.020 PL CCACTT 1444.51 1371 0.949 −0.052 PL CCACTA 779.01 729 0.936 −0.066 PL CCTCTC 2170.57 1934 0.891 −0.115 PL CCTCTG 4510.71 3745 0.830 −0.186 PL CCATTG 1415.38 1172 0.828 −0.189 PL CCCCTT 1671.10 1324 0.792 −0.233 PL CCGCTA 326.54 255 0.781 −0.247 PL CCCCTA 901.21 689 0.765 −0.268 PL CCACTG 4353.41 3218 0.739 −0.302 PL CCCTTA 974.69 709 0.727 −0.318 PL CCACTC 2094.88 1475 0.704 −0.351 PL CCGTTG 593.29 402 0.678 −0.389 PL CCGCTT 605.50 402 0.664 −0.410 PL CCGTTA 353.17 157 0.445 −0.811 PM CCCATG 2307.54 3923 1.700 0.531 PM CCAATG 1994.65 1552 0.778 −0.251 PM CCGATG 836.10 520 0.622 −0.475 PM CCTATG 2066.72 1210 0.585 −0.535 PN CCCAAC 2313.61 4255 1.839 0.609 PN CCAAAT 1815.81 2453 1.351 0.301 PN CCCAAT 2100.65 2296 1.093 0.089 PN CCAAAC 1999.90 1735 0.868 −0.142 PN CCTAAT 1881.42 1342 0.713 −0.338 PN CCTAAC 2072.16 997 0.481 −0.732 PN CCGAAT 761.14 340 0.447 −0.806 PN CCGAAC 838.30 365 0.435 −0.831 PP CCGCCG 608.57 2335 3.837 1.345 PP CCGCCC 1679.58 2697 1.606 0.474 PP CCCCCG 1679.58 2420 1.441 0.365 PP CCTCCA 3588.72 4314 1.202 0.184 PP CCTCCT 3718.39 4305 1.158 0.146 PP CCACCA 3463.58 3850 1.112 0.106 PP CCACCT 3588.72 3798 1.058 0.057 PP CCCCCA 4006.89 4095 1.022 0.022 PP CCACCC 4006.89 3595 0.897 −0.108 PP CCGCCA 1451.84 1280 0.882 −0.126 PP CCACCG 1451.84 1252 0.862 −0.148 PP CCGCCT 1504.30 1286 0.855 −0.157 PP CCTCCC 4151.67 3338 0.804 −0.218 PP CCTCCG 1504.30 1152 0.766 −0.267 PP CCCCCT 4151.67 3160 0.761 −0.273 PP CCCCCC 4635.43 2315 0.499 −0.694 PQ CCCCAG 5063.98 6421 1.268 0.237 PQ CCGCAG 1834.86 2187 1.192 0.176 PQ CCTCAA 1624.21 1752 1.079 0.076 PQ CCTCAG 4535.49 4221 0.931 −0.072 PQ CCACAA 1567.57 1405 0.896 −0.109 PQ CCACAG 4377.33 3670 0.838 −0.176 PQ CCCCAA 1813.47 1497 0.825 −0.192 PQ CCGCAA 657.08 321 0.489 −0.716 PR CCGCGC 563.43 1094 1.942 0.664 PR CCGCGG 616.23 1113 1.806 0.591 PR CCCAGG 1683.86 2927 1.738 0.553 PR CCCCGG 1700.71 2608 1.533 0.428 PR CCCCGC 1555.00 1979 1.273 0.241 PR CCCCGA 921.92 1166 1.265 0.235 PR CCTCGA 825.71 1015 1.229 0.206 PR CCAAGA 1482.62 1608 1.085 0.081 PR CCTCGT 596.27 644 1.080 0.077 PR CCCAGA 1715.19 1801 1.050 0.049 PR CCGAGG 610.12 636 1.042 0.042 PR CCTCGG 1523.22 1511 0.992 −0.008 PR CCCCGT 665.75 655 0.984 −0.016 PR CCAAGG 1455.54 1347 0.925 −0.077 PR CCACGA 796.91 632 0.793 −0.232 PR CCGCGT 241.23 191 0.792 −0.233 PR CCACGT 575.48 418 0.726 −0.320 PR CCACGG 1470.10 1040 0.707 −0.346 PR CCGCGA 334.04 226 0.677 −0.391 PR CCTCGC 1392.72 838 0.602 −0.508 PR CCACGC 1344.15 701 0.522 −0.651 PR CCGAGA 621.48 308 0.496 −0.702 PR CCTAGA 1536.19 692 0.450 −0.797 PR CCTAGG 1508.13 586 0.389 −0.945 PS CCCAGC 3196.25 6398 2.002 0.694 PS CCCTCG 746.03 1385 1.856 0.619 PS CCGTCG 270.31 483 1.787 0.580 PS CCCAGT 2016.53 2743 1.360 0.308 PS CCTTCA 1776.97 2263 1.274 0.242 PS CCTTCT 2198.02 2711 1.233 0.210 PS CCCTCC 2821.16 3353 1.189 0.173 PS CCATCA 1715.00 1819 1.061 0.059 PS CCATCT 2121.37 2183 1.029 0.029 PS CCTTCC 2526.74 2594 1.027 0.026 PS CCGTCC 1022.21 1048 1.025 0.025 PS CCCTCA 1984.02 1945 0.980 −0.020 PS CCAAGT 1743.10 1582 0.908 −0.097 PS CCCTCT 2454.14 2113 0.861 −0.150 PS CCTTCG 668.17 552 0.826 −0.191 PS CCATCC 2438.63 1995 0.818 −0.201 PS CCGAGC 1158.11 885 0.764 −0.269 PS CCATCG 644.87 475 0.737 −0.306 PS CCAAGC 2762.85 1659 0.600 −0.510 PS CCGTCT 889.22 523 0.588 −0.531 PS CCGAGT 730.66 371 0.508 −0.678 PS CCGTCA 718.88 364 0.506 −0.681 PS CCTAGT 1806.08 860 0.476 −0.742 PS CCTAGC 2862.68 968 0.338 −1.084 PT CCCACG 829.55 1764 2.126 0.754 PT CCCACC 2525.29 4586 1.816 0.597 PT CCCACA 2044.32 2719 1.330 0.285 PT CCCACT 1807.85 2282 1.262 0.233 PT CCAACA 1767.12 1895 1.072 0.070 PT CCAACT 1562.71 1593 1.019 0.019 PT CCGACG 300.57 305 1.015 0.015 PT CCTACT 1619.18 1252 0.773 −0.257 PT CCAACC 2182.87 1514 0.694 −0.366 PT CCTACA 1830.97 1241 0.678 −0.389 PT CCGACC 915.00 592 0.647 −0.435 PT CCAACG 717.06 463 0.646 −0.437 PT CCTACC 2261.75 1251 0.553 −0.592 PT CCGACT 655.05 342 0.522 −0.650 PT CCGACA 740.73 352 0.475 −0.744 PT CCTACG 742.97 352 0.474 −0.747 PV CCTGTT 1493.79 2375 1.590 0.464 PV CCTGTA 969.97 1482 1.528 0.424 PV CCAGTA 936.15 1352 1.444 0.368 PV CCTGTG 3783.57 5362 1.417 0.349 PV CCAGTT 1441.70 2038 1.414 0.346 PV CCTGTC 1912.53 2666 1.394 0.332 PV CCGGTG 1530.67 1911 1.248 0.222 PV CCAGTG 3651.63 3787 1.037 0.036 PV CCAGTC 1845.84 1863 1.009 0.009 PV CCGGTC 773.73 778 1.006 0.006 PV CCCGTG 4224.44 2576 0.610 −0.495 PV CCGGTT 604.32 351 0.581 −0.543 PV CCGGTA 392.41 215 0.548 −0.602 PV CCCGTC 2135.39 1084 0.508 −0.678 PV CCCGTT 1667.85 391 0.234 −1.451 PV CCCGTA 1083.00 216 0.199 −1.612 PW CCCTGG 1769.80 2753 1.556 0.442 PW CCGTGG 641.26 661 1.031 0.030 PW CCATGG 1529.83 1060 0.693 −0.367 PW CCTTGG 1585.10 1052 0.664 −0.410 PY CCCTAC 2166.25 3378 1.559 0.444 PY CCCTAT 1760.24 2097 1.191 0.175 PY CCTTAT 1576.54 1702 1.080 0.077 PY CCATAT 1521.56 1513 0.994 −0.006 PY CCTTAC 1940.18 1485 0.765 −0.267 PY CCGTAC 784.91 592 0.754 −0.282 PY CCGTAT 637.80 429 0.673 −0.397 PY CCATAC 1872.52 1064 0.568 −0.565 QA CAAGCA 1597.87 2339 1.464 0.381 QA CAAGCT 1825.31 2409 1.320 0.277 QA CAGGCG 2095.55 2271 1.084 0.080 QA CAGGCC 7750.37 7695 0.993 −0.007 QA CAAGCC 2775.49 2655 0.957 −0.044 QA CAGGCT 5097.04 4584 0.899 −0.106 QA CAGGCA 4461.94 3943 0.884 −0.124 QA CAAGCG 750.44 458 0.610 −0.494 QC CAGTGT 2490.13 2791 1.121 0.114 QC CAGTGC 2956.40 3260 1.103 0.098 QC CAATGT 891.74 822 0.922 −0.081 QC CAATGC 1058.72 524 0.495 −0.703 QD CAAGAT 2128.42 3326 1.563 0.446 QD CAAGAC 2404.29 2506 1.042 0.041 QD CAGGAC 6713.82 6642 0.989 −0.011 QD CAGGAT 5943.46 4716 0.793 −0.231 QE CAAGAA 3247.03 5286 1.628 0.487 QE CAGGAG 12125.58 12556 1.035 0.035 QE CAAGAG 4342.30 4206 0.969 −0.032 QE CAGGAA 9067.09 6734 0.743 −0.297 QF CAGTTT 3509.26 4032 1.149 0.139 QF CAGTTC 4016.64 4205 1.047 0.046 QF CAATTT 1256.70 1156 0.920 −0.084 QF CAATTC 1438.40 828 0.576 −0.552 QG CAAGGA 1440.03 2837 1.970 0.678 QG CAAGGT 932.30 1506 1.615 0.480 QG CAAGGG 1405.83 1700 1.209 0.190 QG CAAGGC 1952.47 2192 1.123 0.116 QG CAGGGC 5452.14 5605 1.028 0.028 QG CAGGGT 2603.39 2292 0.880 −0.127 QG CAGGGA 4021.17 2871 0.714 −0.337 QG CAGGGG 3925.67 2730 0.695 −0.363 QH CAACAT 1067.82 1364 1.277 0.245 QH CAGCAC 4111.88 4483 1.090 0.086 QH CAGCAT 2981.80 2794 0.937 −0.065 QH CAACAC 1472.51 993 0.674 −0.394 QI CAAATA 656.37 1125 1.714 0.539 QI CAAATT 1427.17 1667 1.168 0.155 QI CAGATC 5039.60 5197 1.031 0.031 QI CAGATA 1832.87 1802 0.983 −0.017 QI CAGATT 3985.26 3693 0.927 −0.076 QI CAAATC 1804.74 1262 0.699 −0.358 QK CAGAAG 8990.94 9726 1.082 0.079 QK CAAAAA 2486.09 2610 1.050 0.049 QK CAGAAA 6942.22 6532 0.941 −0.061 QK CAAAAG 3219.76 2771 0.861 −0.150 QL CAGCTG 10304.18 12629 1.226 0.203 QL CAACTA 660.31 798 1.209 0.189 QL CAACTT 1224.39 1479 1.208 0.189 QL CAGCTC 4958.40 5986 1.207 0.188 QL CAGCTA 1843.86 2002 1.086 0.082 QL CAGCTT 3419.03 3476 1.017 0.017 QL CAATTA 714.15 642 0.899 −0.107 QL CAGTTG 3350.09 2597 0.775 −0.255 QL CAGTTA 1994.20 1518 0.761 −0.273 QL CAACTC 1775.66 1279 0.720 −0.328 QL CAACTG 3690.04 2093 0.567 −0.567 QL CAATTG 1199.70 635 0.529 −0.636 QM CAGATG 5587.91 5592 1.001 0.001 QM CAAATG 2001.09 1997 0.998 −0.002 QN CAAAAT 1720.47 2394 1.391 0.330 QN CAGAAC 5291.34 5195 0.982 −0.018 QN CAGAAT 4804.30 4430 0.922 −0.081 QN CAAAAC 1894.89 1692 0.893 −0.113 QP CAGCCG 1816.66 2237 1.231 0.208 QP CAGCCC 5013.75 6143 1.225 0.203 QP CAGCCT 4490.51 4526 1.008 0.008 QP CAGCCA 4333.91 4235 0.977 −0.023 QP CAACCA 1552.02 1441 0.928 −0.074 QP CAACCT 1608.10 1304 0.811 −0.210 QP CAACCC 1795.48 1132 0.630 −0.461 QP CAACCG 650.57 243 0.374 −0.985 QQ CAACAA 1545.49 1866 1.207 0.188 QQ CAGCAG 12051.19 13131 1.090 0.086 QQ CAGCAA 4315.66 4034 0.935 −0.067 QQ CAACAG 4315.66 3197 0.741 −0.300 QR CAAAGA 1214.45 1863 1.534 0.428 QR CAGAGG 3329.32 4331 1.301 0.263 QR CAAAGG 1192.27 1360 1.141 0.132 QR CAGAGA 3391.27 3777 1.114 0.108 QR CAGCGC 3074.54 3169 1.031 0.030 QR CAGCGG 3362.63 3352 0.997 −0.003 QR CAGCGT 1316.32 1215 0.923 −0.080 QR CAGCGA 1822.82 1469 0.806 −0.216 QR CAACGT 471.39 327 0.694 −0.366 QR CAACGA 652.77 413 0.633 −0.458 QR CAACGG 1204.20 453 0.376 −0.978 QR CAACGC 1101.03 404 0.367 −1.003 QS CAAAGT 904.91 1408 1.556 0.442 QS CAGAGC 4005.17 5248 1.310 0.270 QS CAGAGT 2526.89 2963 1.173 0.159 QS CAAAGC 1434.30 1465 1.021 0.021 QS CAGTCG 934.84 923 0.987 −0.013 QS CAGTCA 2486.15 2379 0.957 −0.044 QS CAGTCT 3075.24 2806 0.912 −0.092 QS CAATCA 890.32 781 0.877 −0.131 QS CAGTCC 3535.16 3051 0.863 −0.147 QS CAATCT 1101.28 765 0.695 −0.364 QS CAATCC 1265.98 587 0.464 −0.769 QS CAATCG 334.78 119 0.355 −1.034 QT CAAACT 1116.05 1463 1.311 0.271 QT CAAACA 1262.03 1602 1.269 0.239 QT CAGACG 1430.02 1665 1.164 0.152 QT CAGACC 4353.25 4301 0.988 −0.012 QT CAGACA 3524.12 3445 0.978 −0.023 QT CAGACT 3116.48 2792 0.896 −0.110 QT CAAACC 1558.95 1232 0.790 −0.235 QT CAAACG 512.11 373 0.728 −0.317 QV CAAGTA 657.01 1210 1.842 0.611 QV CAAGTT 1011.82 1737 1.717 0.540 QV CAAGTC 1295.45 1468 1.133 0.125 QV CAAGTG 2562.79 2712 1.058 0.057 QV CAGGTG 7156.41 7062 0.987 −0.013 QV CAGGTC 3617.45 3213 0.888 −0.119 QV CAGGTT 2825.43 2269 0.803 −0.219 QV CAGGTA 1834.65 1290 0.703 −0.352 QW CAGTGG 3057.92 3447 1.127 0.120 QW CAATGG 1095.08 706 0.645 −0.439 QY CAATAT 1029.01 1120 1.088 0.085 QY CAGTAC 3536.21 3820 1.080 0.077 QY CAGTAT 2873.43 2979 1.037 0.036 QY CAATAC 1266.36 786 0.621 −0.477 RA CGGGCG 659.18 1185 1.798 0.587 RA CGGGCC 2437.97 3513 1.441 0.365 RA AGAGCA 1415.51 1970 1.392 0.331 RA CGCGCG 602.71 827 1.372 0.316 RA CGTGCC 954.35 1266 1.327 0.283 RA CGAGCA 760.84 970 1.275 0.243 RA CGAGCT 869.13 1108 1.275 0.243 RA CGAGCC 1321.57 1595 1.207 0.188 RA AGAGCT 1616.99 1949 1.205 0.187 RA CGTGCT 627.63 744 1.185 0.170 RA CGGGCA 1403.55 1612 1.149 0.138 RA CGTGCA 549.43 570 1.037 0.037 RA CGTGCG 258.04 250 0.969 −0.032 RA CGAGCG 357.33 341 0.954 −0.047 RA AGGGCC 2413.81 2173 0.900 −0.105 RA AGAGCC 2458.73 2202 0.896 −0.110 RA CGGGCT 1603.33 1435 0.895 −0.111 RA AGGGCA 1389.65 1242 0.894 −0.112 RA AGGGCT 1587.45 1311 0.826 −0.191 RA AGGGCG 652.65 524 0.803 −0.220 RA CGCGCC 2229.09 1712 0.768 −0.264 RA AGAGCG 664.79 384 0.578 −0.549 RA CGCGCA 1283.30 331 0.258 −1.355 RA CGCGCT 1465.97 369 0.252 −1.379 RC CGCTGC 986.26 2873 2.913 1.069 RC CGCTGT 830.71 1313 1.581 0.458 RC CGTTGT 355.66 320 0.900 −0.106 RC CGTTGC 422.25 372 0.881 −0.127 RC AGATGT 916.29 806 0.880 −0.128 RC CGATGT 492.51 421 0.855 −0.157 RC AGGTGT 899.55 671 0.746 −0.293 RC AGGTGC 1067.99 758 0.710 −0.343 RC CGATGC 584.73 381 0.652 −0.428 RC CGGTGC 1078.67 660 0.612 −0.491 RC AGATGC 1087.86 642 0.590 −0.527 RC CGGTGT 908.55 414 0.456 −0.786 RD AGAGAT 2027.66 2952 1.456 0.376 RD CGGGAC 2271.13 3231 1.423 0.353 RD CGAGAT 1089.87 1500 1.376 0.319 RD CGAGAC 1231.14 1693 1.375 0.319 RD CGTGAC 889.05 1044 1.174 0.161 RD AGAGAC 2290.48 2433 1.062 0.060 RD CGTGAT 787.04 833 1.058 0.057 RD AGGGAC 2248.63 2322 1.033 0.032 RD AGGGAT 1990.62 1732 0.870 −0.139 RD CGGGAT 2010.54 1606 0.799 −0.225 RD CGCGAC 2076.56 1092 0.526 −0.643 RD CGCGAT 1838.29 313 0.170 −1.770 RE AGAGAA 2644.21 4195 1.586 0.462 RE CGGGAG 3506.29 5344 1.524 0.421 RE CGAGAG 1900.69 2475 1.302 0.264 RE CGAGAA 1421.27 1844 1.297 0.260 RE CGTGAG 1372.55 1453 1.059 0.057 RE AGGGAG 3471.55 3469 0.999 −0.001 RE AGAGAG 3536.15 3392 0.959 −0.042 RE CGTGAA 1026.35 947 0.923 −0.080 RE AGGGAA 2595.91 2343 0.903 −0.103 RE CGGGAA 2621.88 2131 0.813 −0.207 RE CGCGAG 3205.89 1839 0.574 −0.556 RE CGCGAA 2397.25 268 0.112 −2.191 RF CGCTTC 1446.49 3411 2.358 0.858 RF CGTTTC 619.29 823 1.329 0.284 RF CGTTTT 541.07 705 1.303 0.265 RF AGATTT 1393.96 1531 1.098 0.094 RF CGCTTT 1263.77 1366 1.081 0.078 RF CGATTT 749.26 772 1.030 0.030 RF AGGTTT 1368.50 1295 0.946 −0.055 RF AGGTTC 1566.36 1192 0.761 −0.273 RF CGATTC 857.59 632 0.737 −0.305 RF CGGTTC 1582.03 951 0.601 −0.509 RF AGATTC 1595.50 944 0.592 −0.525 RF CGGTTT 1382.19 744 0.538 −0.619 RG CGTGGT 370.38 685 1.849 0.615 RG CGTGGG 558.50 980 1.755 0.562 RG CGTGGC 775.66 1315 1.695 0.528 RG CGAGGA 792.21 1266 1.598 0.469 RG CGAGGG 773.39 1219 1.576 0.455 RG AGAGGA 1473.87 2281 1.548 0.437 RG CGAGGT 512.89 789 1.538 0.431 RG CGGGGC 1981.48 2952 1.490 0.399 RG CGTGGA 572.08 844 1.475 0.389 RG CGAGGC 1074.12 1569 1.461 0.379 RG AGAGGT 954.21 1128 1.182 0.167 RG CGGGGT 946.15 918 0.970 −0.030 RG CGCGGC 1811.72 1574 0.869 −0.141 RG AGGGGC 1961.86 1660 0.846 −0.167 RG AGAGGC 1998.36 1680 0.841 −0.174 RG AGAGGG 1438.87 1203 0.836 −0.179 RG AGGGGT 936.78 777 0.829 −0.187 RG CGGGGG 1426.72 1146 0.803 −0.219 RG CGGGGA 1461.42 1140 0.780 −0.248 RG CGCGGG 1304.48 904 0.693 −0.367 RG AGGGGA 1446.94 923 0.638 −0.450 RG AGGGGG 1412.58 683 0.484 −0.727 RG CGCGGT 865.09 248 0.287 −1.249 RG CGCGGA 1336.22 302 0.226 −1.487 RH CGCCAC 1288.00 1861 1.445 0.368 RH CGGCAC 1408.69 1707 1.212 0.192 RH AGACAT 1030.24 1201 1.166 0.153 RH CGTCAT 399.89 447 1.118 0.111 RH AGGCAT 1011.41 988 0.977 −0.023 RH CGACAT 553.75 530 0.957 −0.044 RH AGGCAC 1394.73 1292 0.926 −0.077 RH AGACAC 1420.69 1212 0.853 −0.159 RH CGTCAC 551.44 468 0.849 −0.164 RH CGACAC 763.62 614 0.804 −0.218 RH CGCCAT 934.02 728 0.779 −0.249 RH CGGCAT 1021.53 730 0.715 −0.336 RI CGCATC 1625.56 2948 1.814 0.595 RI AGAATA 652.11 1175 1.802 0.589 RI AGAATT 1417.90 2185 1.541 0.432 RI AGGATA 640.20 804 1.256 0.228 RI CGAATA 350.51 439 1.252 0.225 RI CGAATT 762.13 850 1.115 0.109 RI AGGATT 1392.00 1366 0.981 −0.019 RI AGGATC 1760.27 1662 0.944 −0.057 RI CGAATC 963.75 802 0.832 −0.184 RI CGGATC 1777.88 1479 0.832 −0.184 RI AGAATC 1793.03 1389 0.775 −0.255 RI CGTATT 550.36 408 0.741 −0.299 RI CGCATT 1285.48 913 0.710 −0.342 RI CGGATA 646.60 451 0.697 −0.360 RI CGTATC 695.96 440 0.632 −0.459 RI CGTATA 253.12 152 0.601 −0.510 RI CGGATT 1405.93 825 0.587 −0.533 RI CGCATA 591.21 276 0.467 −0.762 RK AGGAAG 3199.71 4856 1.518 0.417 RK AGGAAA 2470.61 3737 1.513 0.414 RK AGAAAA 2516.58 3482 1.384 0.325 RK CGCAAG 2954.85 2981 1.009 0.009 RK CGGAAG 3231.73 3225 0.998 −0.002 RK AGAAAG 3259.25 2909 0.893 −0.114 RK CGAAAA 1352.67 1189 0.879 −0.129 RK CGGAAA 2495.33 1834 0.735 −0.308 RK CGAAAG 1751.85 1265 0.722 −0.326 RK CGTAAA 976.81 566 0.579 −0.546 RK CGCAAA 2281.54 1209 0.530 −0.635 RK CGTAAG 1265.08 503 0.398 −0.922 RL CGCCTC 1491.12 2511 1.684 0.521 RL CGCCTG 3098.73 4809 1.552 0.439 RL CGGCTG 3389.08 5029 1.484 0.395 RL CGGCTC 1630.84 2301 1.411 0.344 RL CGTTTA 256.76 337 1.313 0.272 RL AGATTA 661.49 862 1.303 0.265 RL CGTCTT 440.20 562 1.277 0.244 RL CGTCTA 237.40 296 1.247 0.221 RL CGTTTG 431.33 526 1.219 0.198 RL CGTCTC 638.40 723 1.133 0.124 RL AGGCTA 600.44 669 1.114 0.108 RL AGACTT 1134.11 1227 1.082 0.079 RL AGGCTG 3355.51 3531 1.052 0.051 RL AGACTA 611.62 617 1.009 0.009 RL AGGCTT 1113.39 1104 0.992 −0.008 RL CGACTA 328.75 324 0.986 −0.015 RL CGGCTA 606.45 593 0.978 −0.022 RL CGTCTG 1326.68 1281 0.966 −0.035 RL AGGCTC 1614.68 1540 0.954 −0.047 RL CGATTA 355.55 337 0.948 −0.054 RL CGACTT 609.59 576 0.945 −0.057 RL CGCCTA 554.49 501 0.904 −0.101 RL AGGTTA 649.40 586 0.902 −0.103 RL CGCCTT 1028.19 862 0.838 −0.176 RL CGCTTG 1007.46 804 0.798 −0.226 RL CGGCTT 1124.53 866 0.770 −0.261 RL AGATTG 1111.24 839 0.755 −0.281 RL CGACTC 884.04 663 0.750 −0.288 RL AGGTTG 1090.94 774 0.709 −0.343 RL AGACTC 1644.73 1142 0.694 −0.365 RL CGATTG 597.29 408 0.683 −0.381 RL CGACTG 1837.15 1128 0.614 −0.488 RL CGCTTA 599.71 345 0.575 −0.553 RL CGGTTG 1101.86 566 0.514 −0.666 RL AGACTG 3417.95 1701 0.498 −0.698 RL CGGTTA 655.90 297 0.453 −0.792 RM CGCATG 1558.32 1961 1.258 0.230 RM AGGATG 1687.45 1974 1.170 0.157 RM CGAATG 923.88 932 1.009 0.009 RM AGAATG 1718.85 1690 0.983 −0.017 RM CGGATG 1704.33 1374 0.806 −0.215 RM CGTATG 667.17 329 0.493 −0.707 RN AGAAAT 1568.88 2627 1.674 0.515 RN AGGAAC 1696.37 2200 1.297 0.260 RN AGGAAT 1540.22 1796 1.166 0.154 RN AGAAAC 1727.93 1949 1.128 0.120 RN CGAAAT 843.28 930 1.103 0.098 RN CGCAAC 1566.55 1575 1.005 0.005 RN CGGAAC 1713.34 1621 0.946 −0.055 RN CGAAAC 928.77 784 0.844 −0.169 RN CGGAAT 1555.63 1002 0.644 −0.440 RN CGTAAT 608.96 340 0.558 −0.583 RN CGCAAT 1422.36 711 0.500 −0.693 RN CGTAAC 670.70 308 0.459 −0.778 RP CGGCCG 587.88 1226 2.085 0.735 RP CGGCCC 1622.47 2939 1.811 0.594 RP CGCCCG 537.51 717 1.334 0.288 RP AGGCCC 1606.39 1982 1.234 0.210 RP AGGCCG 582.05 666 1.144 0.135 RP AGGCCT 1438.75 1642 1.141 0.132 RP AGGCCA 1388.57 1511 1.088 0.084 RP CGTCCT 568.84 589 1.035 0.035 RP AGACCA 1414.41 1387 0.981 −0.020 RP CGGCCT 1453.14 1390 0.957 −0.044 RP AGACCT 1465.52 1398 0.954 −0.047 RP CGTCCC 635.12 582 0.916 −0.087 RP CGGCCA 1402.47 1285 0.916 −0.087 RP CGCCCC 1483.46 1320 0.890 −0.117 RP CGTCCA 549.00 487 0.887 −0.120 RP AGACCC 1636.29 1283 0.784 −0.243 RP CGACCA 760.25 591 0.777 −0.252 RP CGACCC 879.51 671 0.763 −0.271 RP CGACCT 787.72 580 0.736 −0.306 RP CGCCCA 1282.31 887 0.692 −0.369 RP CGTCCG 230.13 159 0.691 −0.370 RP CGCCCT 1328.65 830 0.625 −0.470 RP CGACCG 318.68 184 0.577 −0.549 RP AGACCG 592.88 246 0.415 −0.880 RQ AGACAA 1054.78 1456 1.380 0.322 RQ CGGCAG 2920.52 3950 1.352 0.302 RQ CGCCAG 2670.31 3160 1.183 0.168 RQ AGGCAA 1035.51 1177 1.137 0.128 RQ AGGCAG 2891.59 3013 1.042 0.041 RQ CGACAA 566.95 522 0.921 −0.083 RQ CGTCAG 1143.25 953 0.834 −0.182 RQ CGTCAA 409.41 327 0.799 −0.225 RQ CGACAG 1583.16 1249 0.789 −0.237 RQ CGGCAA 1045.87 763 0.730 −0.315 RQ AGACAG 2945.39 2062 0.700 −0.357 RQ CGCCAA 956.27 591 0.618 −0.481 RR CGCCGC 1172.08 2232 1.904 0.644 RR CGGCGG 1402.02 2316 1.652 0.502 RR AGAAGA 1426.00 2307 1.618 0.481 RR CGGCGC 1281.90 2064 1.610 0.476 RR AGGAGG 1374.38 1973 1.436 0.362 RR CGCCGG 1281.90 1679 1.310 0.270 RR CGAAGA 766.48 987 1.288 0.253 RR AGGAGA 1399.95 1758 1.256 0.228 RR CGCAGG 1269.20 1565 1.233 0.209 RR CGGAGG 1388.13 1670 1.203 0.185 RR CGTCGT 214.84 228 1.061 0.059 RR CGAAGG 752.48 770 1.023 0.023 RR CGCCGT 501.81 502 1.000 0.000 RR AGAAGG 1399.95 1325 0.946 −0.055 RR CGGCGT 548.83 498 0.907 −0.097 RR CGTCGA 297.51 265 0.891 −0.116 RR CGGCGA 760.01 675 0.888 −0.119 RR CGTCGC 501.81 438 0.873 −0.136 RR AGGCGG 1388.13 1177 0.848 −0.165 RR CGTCGG 548.83 450 0.820 −0.199 RR CGACGT 297.51 241 0.810 −0.211 RR CGCCGA 694.89 547 0.787 −0.239 RR AGGCGA 752.48 570 0.757 −0.278 RR CGGAGA 1413.96 1068 0.755 −0.281 RR AGACGA 766.48 557 0.727 −0.319 RR AGGCGT 543.39 383 0.705 −0.350 RR AGGCGC 1269.20 889 0.700 −0.356 RR AGACGT 553.50 376 0.679 −0.387 RR CGACGA 411.98 272 0.660 −0.415 RR CGCAGA 1292.82 771 0.596 −0.517 RR CGACGG 760.01 411 0.541 −0.615 RR CGACGC 694.89 368 0.530 −0.636 RR CGTAGA 553.50 271 0.490 −0.714 RR CGTAGG 543.39 235 0.432 −0.838 RR AGACGC 1292.82 524 0.405 −0.903 RR AGACGG 1413.96 569 0.402 −0.910 RS CGCTCG 332.61 817 2.456 0.899 RS CGCAGC 1425.00 2853 2.002 0.694 RS CGCTCC 1257.78 2184 1.736 0.552 RS AGAAGT 991.66 1532 1.545 0.435 RS CGTTCT 468.44 687 1.467 0.383 RS CGAAGT 533.02 728 1.366 0.312 RS CGTTCC 538.50 707 1.313 0.272 RS AGGAGC 1543.09 1992 1.291 0.255 RS CGTTCA 378.71 471 1.244 0.218 RS CGGAGC 1558.53 1856 1.191 0.175 RS AGGAGT 973.54 1071 1.100 0.095 RS AGAAGC 1571.80 1628 1.036 0.035 RS AGATCA 975.67 1000 1.025 0.025 RS CGAAGC 844.85 859 1.017 0.017 RS CGCTCA 884.55 860 0.972 −0.028 RS CGCAGT 899.04 853 0.949 −0.053 RS AGATCT 1206.86 1106 0.916 −0.087 RS CGCTCT 1094.14 942 0.861 −0.150 RS CGTTCG 142.40 121 0.850 −0.163 RS AGGTCA 957.85 808 0.844 −0.170 RS CGATCA 524.43 416 0.793 −0.232 RS AGGTCT 1184.81 939 0.793 −0.233 RS AGGTCG 360.17 284 0.789 −0.238 RS CGATCT 648.69 497 0.766 −0.266 RS AGGTCC 1362.00 1036 0.761 −0.274 RS CGGAGT 983.28 745 0.758 −0.278 RS CGTAGT 384.91 278 0.722 −0.325 RS CGGTCG 363.77 235 0.646 −0.437 RS CGATCC 745.70 455 0.610 −0.494 RS AGATCC 1387.35 830 0.598 −0.514 RS CGGTCC 1375.63 821 0.597 −0.516 RS CGATCG 197.19 107 0.543 −0.611 RS CGGTCA 967.43 507 0.524 −0.646 RS CGTAGC 610.09 317 0.520 −0.655 RS AGATCG 366.87 177 0.482 −0.729 RS CGGTCT 1196.66 518 0.433 −0.837 RT CGCACG 450.78 858 1.903 0.644 RT AGAACT 1083.61 1467 1.354 0.303 RT CGCACC 1372.27 1821 1.327 0.283 RT AGGACG 488.14 646 1.323 0.280 RT AGGACT 1063.81 1389 1.306 0.267 RT AGAACA 1225.34 1575 1.285 0.251 RT AGGACA 1202.96 1523 1.266 0.236 RT AGGACC 1485.98 1773 1.193 0.177 RT CGGACG 493.02 537 1.089 0.085 RT CGAACA 658.62 661 1.004 0.004 RT CGAACT 582.44 556 0.955 −0.046 RT CGGACC 1500.85 1408 0.938 −0.064 RT CGCACA 1110.90 984 0.886 −0.121 RT CGGACA 1215.00 949 0.781 −0.247 RT AGAACC 1513.63 1166 0.770 −0.261 RT CGTACT 420.60 313 0.744 −0.295 RT CGAACC 813.58 599 0.736 −0.306 RT CGGACT 1074.45 712 0.663 −0.411 RT CGCACT 982.40 638 0.649 −0.432 RT CGTACC 587.52 361 0.614 −0.487 RT AGAACG 497.22 302 0.607 −0.499 RT CGTACA 475.62 288 0.606 −0.502 RT CGAACG 267.26 154 0.576 −0.551 RT CGTACG 193.00 79 0.409 −0.893 RV CGTGTG 889.90 1699 1.909 0.647 RV CGTGTC 449.83 826 1.836 0.608 RV CGAGTA 315.92 562 1.779 0.576 RV CGTGTA 228.14 391 1.714 0.539 RV CGTGTT 351.34 565 1.608 0.475 RV AGAGTT 905.17 1350 1.491 0.400 RV AGAGTA 587.76 876 1.490 0.399 RV CGAGTC 622.91 914 1.467 0.383 RV CGAGTT 486.53 681 1.400 0.336 RV CGAGTG 1232.31 1576 1.279 0.246 RV CGGGTC 1149.12 1310 1.140 0.131 RV AGGGTC 1137.73 1221 1.073 0.071 RV CGGGTG 2273.30 2328 1.024 0.024 RV AGAGTC 1158.91 1154 0.996 −0.004 RV CGCGTG 2078.54 1725 0.830 −0.186 RV AGGGTA 577.02 471 0.816 −0.203 RV AGAGTG 2292.67 1750 0.763 −0.270 RV CGGGTA 582.79 438 0.752 −0.286 RV AGGGTG 2250.78 1658 0.737 −0.306 RV CGCGTC 1050.67 763 0.726 −0.320 RV AGGGTT 888.63 645 0.726 −0.320 RV CGGGTT 897.52 548 0.611 −0.493 RV CGCGTA 532.86 132 0.248 −1.395 RV CGCGTT 820.63 178 0.217 −1.528 RW CGCTGG 1038.00 2199 2.118 0.751 RW CGTTGG 444.40 380 0.855 −0.157 RW AGGTGG 1124.01 876 0.779 −0.249 RW CGATGG 615.40 466 0.757 −0.278 RW AGATGG 1144.93 804 0.702 −0.353 RW CGGTGG 1135.26 777 0.684 −0.379 RY CGCTAC 1173.12 2612 2.227 0.800 RY CGCTAT 953.25 1198 1.257 0.229 RY CGTTAC 502.25 565 1.125 0.118 RY CGTTAT 408.12 459 1.125 0.117 RY AGATAT 1051.45 1018 0.968 −0.032 RY AGATAC 1293.97 1239 0.958 −0.043 RY CGATAT 565.15 509 0.901 −0.105 RY CGATAC 695.51 584 0.840 −0.175 RY AGGTAC 1270.33 1007 0.793 −0.232 RY AGGTAT 1032.24 769 0.745 −0.294 RY CGGTAC 1283.04 856 0.667 −0.405 RY CGGTAT 1042.57 455 0.436 −0.829 SA TCGGCG 241.39 778 3.223 1.170 SA TCGGCC 892.76 1976 2.213 0.795 SA TCAGCA 1366.87 2526 1.848 0.614 SA TCTGCA 1690.75 3035 1.795 0.585 SA TCTGCT 1931.41 3350 1.734 0.551 SA TCAGCT 1561.43 2630 1.684 0.521 SA AGTGCT 1587.01 2487 1.567 0.449 SA AGTGCA 1389.27 2040 1.468 0.384 SA AGTGCC 2413.15 3437 1.424 0.354 SA TCAGCC 2374.25 3294 1.387 0.327 SA TCGGCT 587.12 808 1.376 0.319 SA TCTGCC 2936.83 3480 1.185 0.170 SA TCGGCA 513.97 598 1.163 0.151 SA TCTGCG 794.06 745 0.938 −0.064 SA TCAGCG 641.95 584 0.910 −0.095 SA AGTGCG 652.47 532 0.815 −0.204 SA AGCGCG 1034.18 802 0.775 −0.254 SA AGCGCC 3824.90 2428 0.635 −0.454 SA TCCGCG 912.82 577 0.632 −0.459 SA TCCGCC 3376.05 1230 0.364 −1.010 SA AGCGCT 2515.45 709 0.282 −1.266 SA AGCGCA 2202.02 601 0.273 −1.299 SA TCCGCA 1943.61 476 0.245 −1.407 SA TCCGCT 2220.26 481 0.217 −1.530 SC TCCTGC 1640.34 2828 1.724 0.545 SC AGCTGC 1858.43 3034 1.633 0.490 SC TCCTGT 1381.63 1779 1.288 0.253 SC AGCTGT 1565.33 1922 1.228 0.205 SC TCGTGC 433.77 361 0.832 −0.184 SC TCTTGT 1201.89 941 0.783 −0.245 SC AGTTGT 987.57 698 0.707 −0.347 SC TCGTGT 365.36 225 0.616 −0.485 SC TCATGT 971.65 584 0.601 −0.509 SC TCTTGC 1426.94 758 0.531 −0.633 SC TCATGC 1153.59 525 0.455 −0.787 SC AGTTGC 1172.49 504 0.430 −0.844 SD TCAGAT 1978.63 3706 1.873 0.628 SD AGTGAT 2011.05 3683 1.831 0.605 SD AGTGAC 2271.71 4040 1.778 0.576 SD TCGGAC 840.43 1438 1.711 0.537 SD TCTGAT 2447.46 3578 1.462 0.380 SD TCAGAC 2235.09 2906 1.300 0.262 SD TCGGAT 744.00 840 1.129 0.121 SD TCTGAC 2764.69 2949 1.067 0.065 SD AGCGAC 3600.71 2017 0.560 −0.580 SD TCCGAC 3178.17 1336 0.420 −0.867 SD AGCGAT 3187.56 920 0.289 −1.243 SD TCCGAT 2813.50 660 0.235 −1.450 SE TCAGAA 2420.84 4815 1.989 0.688 SE AGTGAA 2460.50 4686 1.904 0.644 SE TCGGAG 1217.33 2184 1.794 0.584 SE TCTGAA 2994.45 4621 1.543 0.434 SE TCAGAG 3237.43 4683 1.447 0.369 SE AGTGAG 3290.47 4410 1.340 0.293 SE TCTGAG 4004.54 4891 1.221 0.200 SE TCGGAA 910.28 879 0.966 −0.035 SE AGCGAG 5215.47 2961 0.568 −0.566 SE TCCGAG 4603.44 2005 0.436 −0.831 SE AGCGAA 3899.95 847 0.217 −1.527 SE TCCGAA 3442.29 715 0.208 −1.572 SF TCCTTC 2645.79 4407 1.666 0.510 SF AGCTTC 2997.56 3942 1.315 0.274 SF TCATTT 1625.65 1773 1.091 0.087 SF TCCTTT 2311.58 2487 1.076 0.073 SF AGTTTT 1652.29 1695 1.026 0.026 SF AGCTTT 2618.91 2370 0.905 −0.100 SF TCTTTT 2010.85 1809 0.900 −0.106 SF TCTTTC 2301.58 1728 0.751 −0.287 SF AGTTTC 1891.18 1353 0.715 −0.335 SF TCGTTT 611.27 342 0.559 −0.581 SF TCATTC 1860.69 991 0.533 −0.630 SF TCGTTC 699.65 330 0.472 −0.751 SG AGTGGT 1051.00 2094 1.992 0.689 SG TCGGGG 586.31 1117 1.905 0.645 SG TCGGGC 814.29 1487 1.826 0.602 SG AGTGGA 1623.36 2932 1.806 0.591 SG TCAGGA 1597.19 2760 1.728 0.547 SG TCTGGA 1975.64 3391 1.716 0.540 SG AGTGGG 1584.81 2584 1.630 0.489 SG TCTGGG 1928.73 2974 1.542 0.433 SG AGTGGC 2201.05 3314 1.506 0.409 SG TCTGGT 1279.07 1902 1.487 0.397 SG TCAGGG 1559.26 2161 1.386 0.326 SG TCAGGT 1034.06 1351 1.307 0.267 SG TCGGGA 600.57 684 1.139 0.130 SG TCGGGT 388.82 410 1.054 0.053 SG TCTGGC 2678.70 2734 1.021 0.020 SG TCAGGC 2165.57 2114 0.976 −0.024 SG AGCGGC 3488.72 2475 0.709 −0.343 SG AGCGGG 2511.96 1464 0.583 −0.540 SG TCCGGG 2217.18 1117 0.504 −0.686 SG TCCGGC 3079.31 1163 0.378 −0.974 SG AGCGGT 1665.85 536 0.322 −1.134 SG AGCGGA 2573.06 663 0.258 −1.356 SG TCCGGA 2271.11 560 0.247 −1.400 SG TCCGGT 1470.37 359 0.244 −1.410 SH AGCCAC 2202.27 3210 1.458 0.377 SH TCTCAT 1226.22 1426 1.163 0.151 SH TCCCAC 1943.83 2233 1.149 0.139 SH AGTCAT 1007.57 1082 1.074 0.071 SH AGCCAT 1597.01 1606 1.006 0.006 SH TCGCAC 514.03 512 0.996 −0.004 SH TCCCAT 1409.60 1349 0.957 −0.044 SH TCACAT 991.32 929 0.937 −0.065 SH AGTCAC 1389.42 1077 0.775 −0.255 SH TCACAC 1367.03 956 0.699 −0.358 SH TCTCAC 1690.94 1158 0.685 −0.379 SH TCGCAT 372.75 174 0.467 −0.762 SI TCCATC 2374.96 4526 1.906 0.645 SI AGCATC 2690.72 4471 1.662 0.508 SI TCCATT 1878.09 2383 1.269 0.238 SI AGCATT 2127.79 2384 1.120 0.114 SI TCCATA 863.76 963 1.115 0.109 SI AGTATA 617.40 640 1.037 0.036 SI TCAATA 607.45 618 1.017 0.017 SI AGTATT 1342.43 1299 0.968 −0.033 SI AGCATA 978.60 943 0.964 −0.037 SI TCTATA 751.38 658 0.876 −0.133 SI TCTATT 1633.75 1215 0.744 −0.296 SI TCAATT 1320.79 957 0.725 −0.322 SI AGTATC 1697.59 924 0.544 −0.608 SI TCGATA 228.41 109 0.477 −0.740 SI TCTATC 2065.98 958 0.464 −0.769 SI TCGATT 496.64 185 0.373 −0.988 SI TCAATC 1670.22 557 0.333 −1.098 SI TCGATC 628.03 184 0.293 −1.228 SK TCCAAG 3563.99 5021 1.409 0.343 SK TCCAAA 2751.88 3634 1.321 0.278 SK AGCAAG 4037.83 5128 1.270 0.239 SK AGCAAA 3117.75 3736 1.198 0.181 SK TCAAAA 1935.30 2282 1.179 0.165 SK AGTAAA 1967.01 2149 1.093 0.088 SK TCAAAG 2506.42 2082 0.831 −0.186 SK TCTAAA 2393.86 1838 0.768 −0.264 SK TCGAAG 942.46 522 0.554 −0.591 SK AGTAAG 2547.49 1300 0.510 −0.673 SK TCTAAG 3100.32 1569 0.506 −0.681 SK TCGAAA 727.71 331 0.455 −0.788 SL AGTTTA 709.05 1103 1.556 0.442 SL TCGCTG 1355.42 2104 1.552 0.440 SL TCCTTG 1666.44 2462 1.477 0.390 SL TCTTTA 862.92 1267 1.468 0.384 SL AGCCTC 2794.39 4013 1.436 0.362 SL TCTTTG 1449.64 2009 1.386 0.326 SL TCATTA 697.62 862 1.236 0.212 SL AGCCTG 5807.08 7014 1.208 0.189 SL AGTTTG 1191.15 1427 1.198 0.181 SL TCGCTC 652.23 777 1.191 0.175 SL TCTCTA 797.87 950 1.191 0.175 SL TCTCTT 1479.47 1750 1.183 0.168 SL TCCCTG 5125.62 6034 1.177 0.163 SL TCCCTC 2466.46 2805 1.137 0.129 SL TCCTTA 991.98 1076 1.085 0.081 SL AGTCTT 1215.66 1242 1.022 0.021 SL AGCCTT 1926.85 1959 1.017 0.017 SL TCACTA 645.03 630 0.977 −0.024 SL AGCTTG 1888.00 1786 0.946 −0.056 SL TCACTT 1196.06 1111 0.929 −0.074 SL TCCCTT 1700.73 1545 0.908 −0.096 SL TCCCTA 917.19 810 0.883 −0.124 SL AGTCTA 655.60 569 0.868 −0.142 SL TCATTG 1171.95 1015 0.866 −0.144 SL AGCCTA 1039.14 875 0.842 −0.172 SL TCTCTC 2145.58 1760 0.820 −0.198 SL TCTCTG 4458.78 3418 0.767 −0.266 SL AGCTTA 1123.86 758 0.674 −0.394 SL AGTCTC 1763.00 1158 0.657 −0.420 SL TCGTTG 440.67 280 0.635 −0.454 SL TCACTC 1734.58 1100 0.634 −0.455 SL TCACTG 3604.66 2254 0.625 −0.470 SL TCGCTT 449.74 279 0.620 −0.477 SL TCGCTA 242.54 143 0.590 −0.528 SL TCGTTA 262.32 140 0.534 −0.628 SL AGTCTG 3663.72 1808 0.493 −0.706 SM TCCATG 2282.65 3908 1.712 0.538 SM AGCATG 2586.13 3300 1.276 0.244 SM TCAATG 1605.31 1129 0.703 −0.352 SM TCGATG 603.62 365 0.605 −0.503 SM AGTATG 1631.61 966 0.592 −0.524 SM TCTATG 1985.68 1027 0.517 −0.659 SN AGCAAC 2539.42 3717 1.464 0.381 SN TCCAAC 2241.42 3216 1.435 0.361 SN TCAAAT 1431.22 1883 1.316 0.274 SN AGCAAT 2305.68 2513 1.090 0.086 SN TCCAAT 2035.11 2000 0.983 −0.017 SN AGTAAT 1454.67 1425 0.980 −0.021 SN AGTAAC 1602.14 1339 0.836 −0.179 SN TCAAAC 1576.31 1194 0.757 −0.278 SN TCTAAT 1770.34 1297 0.733 −0.311 SN TCTAAC 1949.81 955 0.490 −0.714 SN TCGAAT 538.16 258 0.479 −0.735 SN TCGAAC 592.72 240 0.405 −0.904 SP TCGCCG 282.21 549 1.945 0.665 SP TCGCCC 778.87 1221 1.568 0.450 SP TCCCCG 1067.21 1621 1.519 0.418 SP TCTCCA 2214.76 3119 1.408 0.342 SP AGCCCC 3336.96 4654 1.395 0.333 SP TCTCCT 2294.78 2888 1.259 0.230 SP AGCCCG 1209.10 1432 1.184 0.169 SP TCCCCA 2545.99 2968 1.166 0.153 SP TCACCA 1790.50 1869 1.044 0.043 SP AGCCCT 2988.71 3086 1.033 0.032 SP AGTCCT 1885.59 1904 1.010 0.010 SP TCACCT 1855.20 1752 0.944 −0.057 SP AGCCCA 2884.48 2607 0.904 −0.101 SP TCCCCT 2637.98 2238 0.848 −0.164 SP AGTCCA 1819.84 1473 0.809 −0.211 SP TCGCCT 697.59 562 0.806 −0.216 SP TCGCCA 673.26 541 0.804 −0.219 SP TCTCCC 2562.18 2036 0.795 −0.230 SP TCACCC 2071.37 1568 0.757 −0.278 SP AGTCCC 2105.31 1534 0.729 −0.317 SP TCTCCG 928.37 664 0.715 −0.335 SP TCCCCC 2945.37 2058 0.699 −0.358 SP TCACCG 750.53 426 0.568 −0.566 SP AGTCCG 762.83 319 0.418 −0.872 SQ TCCCAG 4427.95 5592 1.263 0.233 SQ AGCCAG 5016.65 6041 1.204 0.186 SQ TCTCAA 1379.40 1644 1.192 0.175 SQ AGTCAA 1133.44 1293 1.141 0.132 SQ TCACAA 1115.16 1196 1.072 0.070 SQ AGCCAA 1796.52 1819 1.013 0.012 SQ TCCCAA 1585.70 1474 0.930 −0.073 SQ TCTCAG 3851.88 3430 0.890 −0.116 SQ TCGCAG 1170.92 1015 0.867 −0.143 SQ TCACAG 3114.02 2271 0.729 −0.316 SQ AGTCAG 3165.04 2215 0.700 −0.357 SQ TCGCAA 419.32 186 0.444 −0.813 SR AGCCGC 1540.23 2828 1.836 0.608 SR TCCAGG 1472.14 2309 1.568 0.450 SR AGCCGG 1684.56 2353 1.397 0.334 SR TCCCGG 1486.87 1976 1.329 0.284 SR AGCAGG 1667.87 2186 1.311 0.271 SR AGCCGT 659.43 857 1.300 0.262 SR TCGCGC 359.50 446 1.241 0.216 SR TCCAGA 1499.54 1850 1.234 0.210 SR TCAAGA 1054.57 1294 1.227 0.205 SR TCGCGG 393.19 481 1.223 0.202 SR TCCCGC 1359.49 1605 1.181 0.166 SR TCTCGA 701.14 826 1.178 0.164 SR AGTCGT 416.04 484 1.163 0.151 SR TCCCGA 806.00 937 1.163 0.151 SR AGCAGA 1698.90 1925 1.133 0.125 SR AGCCGA 913.16 1020 1.117 0.111 SR TCTCGT 506.32 493 0.974 −0.027 SR AGTCGA 576.12 553 0.960 −0.041 SR TCCCGT 582.04 553 0.950 −0.051 SR TCAAGG 1035.31 922 0.891 −0.116 SR TCGAGG 389.29 324 0.832 −0.184 SR TCTCGG 1293.43 1062 0.821 −0.197 SR TCACGT 409.33 323 0.789 −0.237 SR AGTAGA 1071.85 746 0.696 −0.362 SR TCGCGT 153.92 102 0.663 −0.411 SR AGTCGG 1062.80 675 0.635 −0.454 SR AGTCGC 971.74 591 0.608 −0.497 SR TCACGA 566.83 344 0.607 −0.499 SR TCGAGA 396.54 240 0.605 −0.502 SR TCTAGA 1304.45 750 0.575 −0.553 SR TCGCGA 213.14 115 0.540 −0.617 SR TCTCGC 1182.62 636 0.538 −0.620 SR TCACGG 1045.66 534 0.511 −0.672 SR TCTAGG 1280.62 574 0.448 −0.802 SR TCACGC 956.08 406 0.425 −0.856 SR AGTAGG 1052.27 443 0.421 −0.865 SS AGCAGC 3919.72 7160 1.827 0.602 SS TCGTCG 213.54 376 1.761 0.566 SS TCCTCG 807.53 1302 1.612 0.478 SS TCCAGC 3459.74 4832 1.397 0.334 SS TCTTCA 1868.19 2596 1.390 0.329 SS AGCAGT 2472.97 3417 1.382 0.323 SS TCCTCC 3053.74 4162 1.363 0.310 SS TCTTCT 2310.85 2896 1.253 0.226 SS TCCAGT 2182.77 2691 1.233 0.209 SS TCATCA 1510.32 1795 1.188 0.173 SS AGCTCC 3459.74 4024 1.163 0.151 SS TCATCT 1868.19 2118 1.134 0.126 SS TCCTCA 2147.58 2413 1.124 0.117 SS AGCTCG 914.89 1001 1.094 0.090 SS TCCTCT 2656.45 2744 1.033 0.032 SS TCGTCC 807.53 818 1.013 0.013 SS TCTTCC 2656.45 2600 0.979 −0.021 SS AGTTCT 1898.79 1856 0.977 −0.023 SS AGTTCA 1535.06 1498 0.976 −0.024 SS TCAAGT 1535.06 1404 0.915 −0.089 SS AGCTCA 2433.11 2075 0.853 −0.159 SS AGCTCT 3009.63 2465 0.819 −0.200 SS TCTTCG 702.47 556 0.791 −0.234 SS TCATCC 2147.58 1632 0.760 −0.275 SS AGTAGT 1560.21 1030 0.660 −0.415 SS AGTTCC 2182.77 1405 0.644 −0.441 SS TCGTCT 702.47 434 0.618 −0.482 SS TCATCG 567.91 343 0.604 −0.504 SS TCGTCA 567.91 313 0.551 −0.596 SS TCTAGT 1898.79 957 0.504 −0.685 SS TCGAGC 914.89 440 0.481 −0.732 SS AGTAGC 2472.97 1158 0.468 −0.759 SS TCAAGC 2433.11 1117 0.459 −0.779 SS TCGAGT 577.21 259 0.449 −0.801 SS AGTTCG 577.21 251 0.435 −0.833 SS TCTAGC 3009.63 899 0.299 −1.208 ST TCCACG 785.52 1434 1.826 0.602 ST AGCACC 2709.18 4149 1.531 0.426 ST TCCACC 2391.25 3527 1.475 0.389 ST AGCACG 889.95 1180 1.326 0.282 ST AGCACA 2193.18 2692 1.227 0.205 ST TCCACA 1935.81 2329 1.203 0.185 ST TCCACT 1711.89 1937 1.131 0.124 ST AGCACT 1939.49 2193 1.131 0.123 ST TCAACA 1361.39 1485 1.091 0.087 ST TCAACT 1203.91 1270 1.055 0.053 ST TCTACT 1489.18 1390 0.933 −0.069 ST TCTACA 1683.97 1461 0.868 −0.142 ST AGTACT 1223.64 1036 0.847 −0.166 ST AGTACA 1383.69 1061 0.767 −0.266 ST TCGACG 207.72 145 0.698 −0.359 ST TCTACC 2080.15 1218 0.586 −0.535 ST TCGACC 632.34 365 0.577 −0.550 ST AGTACC 1709.24 976 0.571 −0.560 ST TCGACT 452.69 240 0.530 −0.635 ST TCAACC 1681.68 873 0.519 −0.656 ST TCAACG 552.43 275 0.498 −0.698 ST TCGACA 511.90 236 0.461 −0.774 ST TCTACG 683.32 302 0.442 −0.817 ST AGTACG 561.48 201 0.358 −1.027 SV TCGGTG 935.47 1822 1.948 0.667 SV TCTGTA 788.92 1398 1.772 0.572 SV TCTGTT 1214.96 2136 1.758 0.564 SV TCAGTA 637.79 1121 1.758 0.564 SV AGTGTT 998.32 1719 1.722 0.543 SV TCAGTT 982.23 1591 1.620 0.482 SV TCTGTC 1555.54 2367 1.522 0.420 SV AGTGTC 1278.17 1943 1.520 0.419 SV TCTGTG 3077.33 4672 1.518 0.418 SV AGTGTA 648.24 976 1.506 0.409 SV TCGGTC 472.87 683 1.444 0.368 SV TCAGTG 2487.84 2925 1.176 0.162 SV AGTGTG 2528.60 2901 1.147 0.137 SV TCAGTC 1257.56 1351 1.074 0.072 SV TCGGTA 239.82 231 0.963 −0.037 SV TCGGTT 369.33 266 0.720 −0.328 SV AGCGTC 2025.93 1298 0.641 −0.445 SV TCCGTG 3537.57 2065 0.584 −0.538 SV AGCGTG 4007.89 2221 0.554 −0.590 SV TCCGTC 1788.18 829 0.464 −0.769 SV AGCGTT 1582.36 446 0.282 −1.266 SV TCCGTA 906.91 239 0.264 −1.334 SV TCCGTT 1396.67 329 0.236 −1.446 SV AGCGTA 1027.48 217 0.211 −1.555 SW TCCTGG 1756.97 2825 1.608 0.475 SW AGCTGG 1990.56 2404 1.208 0.189 SW TCGTGG 464.61 444 0.956 −0.045 SW TCTTGG 1528.39 1137 0.744 −0.296 SW TCATGG 1235.61 778 0.630 −0.463 SW AGTTGG 1255.86 644 0.513 −0.668 SY TCCTAC 1871.53 3038 1.623 0.484 SY AGCTAC 2120.35 2864 1.351 0.301 SY TCCTAT 1520.75 1869 1.229 0.206 SY AGCTAT 1722.94 1609 0.934 −0.068 SY AGTTAT 1087.01 1010 0.929 −0.073 SY AGTTAC 1337.74 1153 0.862 −0.149 SY TCATAT 1069.49 897 0.839 −0.176 SY TCTTAT 1322.91 1100 0.832 −0.185 SY TCTTAC 1628.04 1204 0.740 −0.302 SY TCGTAC 494.91 304 0.614 −0.487 SY TCGTAT 402.15 204 0.507 −0.679 SY TCATAC 1316.18 642 0.488 −0.718 TA ACGGCG 348.71 734 2.105 0.744 TA ACAGCA 1829.79 3283 1.794 0.585 TA ACGGCC 1289.71 2090 1.621 0.483 TA ACTGCA 1618.13 2557 1.580 0.458 TA ACAGCT 2090.24 3295 1.576 0.455 TA ACTGCT 1848.45 2764 1.495 0.402 TA ACAGCC 3178.34 3912 1.231 0.208 TA ACGGCA 742.49 804 1.083 0.080 TA ACTGCC 2810.69 3015 1.073 0.070 TA ACGGCT 848.18 804 0.948 −0.053 TA ACAGCG 859.36 803 0.934 −0.068 TA ACTGCG 759.96 623 0.820 −0.199 TA ACCGCG 1061.55 584 0.550 −0.598 TA ACCGCC 3926.11 1648 0.420 −0.868 TA ACCGCA 2260.29 561 0.248 −1.394 TA ACCGCT 2582.01 577 0.223 −1.498 TC ACCTGC 1892.82 3247 1.715 0.540 TC ACCTGT 1594.30 1994 1.251 0.224 TC ACGTGC 621.78 691 1.111 0.106 TC ACGTGT 523.72 484 0.924 −0.079 TC ACTTGT 1141.35 1033 0.905 −0.100 TC ACATGT 1290.64 938 0.727 −0.319 TC ACTTGC 1355.07 815 0.601 −0.508 TC ACATGC 1532.31 750 0.489 −0.714 TD ACAGAT 2415.25 4195 1.737 0.552 TD ACAGAC 2728.31 3765 1.380 0.322 TD ACTGAT 2135.87 2913 1.364 0.310 TD ACGGAC 1107.10 1446 1.306 0.267 TD ACTGAC 2412.71 2615 1.084 0.081 TD ACGGAT 980.07 922 0.941 −0.061 TD ACCGAC 3370.20 1547 0.459 −0.779 TD ACCGAT 2983.49 730 0.245 −1.408 TE ACAGAA 3127.33 5307 1.697 0.529 TE ACGGAG 1697.07 2517 1.483 0.394 TE ACTGAA 2765.58 4093 1.480 0.392 TE ACAGAG 4182.23 5419 1.296 0.259 TE ACTGAG 3698.46 4124 1.115 0.109 TE ACGGAA 1269.01 1080 0.851 −0.161 TE ACCGAG 5166.20 2450 0.474 −0.746 TE ACCGAA 3863.10 779 0.202 −1.601 TF ACCTTC 3026.54 4955 1.637 0.493 TF ACATTT 2140.61 2275 1.063 0.061 TF ACTTTT 1893.00 1904 1.006 0.006 TF ACCTTT 2644.23 2518 0.952 −0.049 TF ACTTTC 2166.69 1822 0.841 −0.173 TF ACGTTT 868.62 650 0.748 −0.290 TF ACGTTC 994.21 666 0.670 −0.401 TF ACATTC 2450.10 1394 0.569 −0.564 TG ACTGGA 1710.74 3660 2.139 0.761 TG ACTGGT 1107.57 1887 1.704 0.533 TG ACAGGA 1934.51 2970 1.535 0.429 TG ACGGGC 1064.34 1583 1.487 0.397 TG ACTGGG 1670.12 2322 1.390 0.330 TG ACGGGG 766.35 1049 1.369 0.314 TG ACAGGT 1252.44 1694 1.353 0.302 TG ACAGGG 1888.57 2148 1.137 0.129 TG ACTGGC 2319.53 2620 1.130 0.122 TG ACAGGC 2622.93 2664 1.016 0.016 TG ACGGGT 508.22 484 0.952 −0.049 TG ACGGGA 784.99 710 0.904 −0.100 TG ACCGGG 2332.90 1093 0.469 −0.758 TG ACCGGC 3240.03 1373 0.424 −0.859 TG ACCGGT 1547.11 355 0.229 −1.472 TG ACCGGA 2389.65 528 0.221 −1.510 TH ACTCAT 1054.95 1291 1.224 0.202 TH ACCCAC 2032.09 2408 1.185 0.170 TH ACGCAC 667.53 764 1.145 0.135 TH ACACAT 1192.94 1186 0.994 −0.006 TH ACTCAC 1454.76 1384 0.951 −0.050 TH ACCCAT 1473.60 1287 0.873 −0.135 TH ACACAC 1645.05 1383 0.841 −0.174 TH ACGCAT 484.07 302 0.624 −0.472 TI ACCATC 2842.70 5915 2.081 0.733 TI ACCATT 2247.97 2878 1.280 0.247 TI ACAATA 836.96 980 1.171 0.158 TI ACCATA 1033.87 1137 1.100 0.095 TI ACAATT 1819.82 1579 0.868 −0.142 TI ACTATA 740.14 642 0.867 −0.142 TI ACTATT 1609.31 1337 0.831 −0.185 TI ACGATA 339.62 190 0.559 −0.581 TI ACGATT 738.45 389 0.527 −0.641 TI ACGATC 933.81 463 0.496 −0.702 TI ACTATC 2035.08 942 0.463 −0.770 TI ACAATC 2301.27 1027 0.446 −0.807 TK ACCAAG 3878.56 6678 1.722 0.543 TK ACCAAA 2994.77 3789 1.265 0.235 TK ACAAAA 2424.38 2546 1.050 0.049 TK ACAAAG 3139.84 2507 0.798 −0.225 TK ACTAAA 2143.95 1684 0.785 −0.241 TK ACGAAG 1274.09 708 0.556 −0.588 TK ACGAAA 983.77 511 0.519 −0.655 TK ACTAAG 2776.65 1193 0.430 −0.845 TL ACGCTG 1815.48 3357 1.849 0.615 TL ACTTTA 765.72 1207 1.576 0.455 TL ACTTTG 1286.34 1876 1.458 0.377 TL ACATTA 865.87 1115 1.288 0.253 TL ACCTTG 1796.82 2257 1.256 0.228 TL ACTCTA 707.99 876 1.237 0.213 TL ACGCTC 873.61 1057 1.210 0.191 TL ACCCTC 2659.44 3133 1.178 0.164 TL ACCCTG 5526.65 6354 1.150 0.140 TL ACTCTT 1312.81 1469 1.119 0.112 TL ACACTA 800.60 799 0.998 −0.002 TL ACGCTA 324.87 307 0.945 −0.057 TL ACCTTA 1069.59 957 0.895 −0.111 TL ACACTT 1484.53 1316 0.886 −0.121 TL ACGTTG 590.25 505 0.856 −0.156 TL ACATTG 1454.60 1210 0.832 −0.184 TL ACCCTT 1833.80 1515 0.826 −0.191 TL ACCCTA 988.95 802 0.811 −0.210 TL ACTCTG 3956.51 3120 0.789 −0.238 TL ACGTTA 351.36 262 0.746 −0.293 TL ACTCTC 1903.88 1391 0.731 −0.314 TL ACGCTT 602.39 427 0.709 −0.344 TL ACACTG 4474.03 3013 0.673 −0.395 TL ACACTC 2152.92 1274 0.592 −0.525 TM ACCATG 2733.42 4467 1.634 0.491 TM ACAATG 2212.81 1641 0.742 −0.299 TM ACGATG 897.92 655 0.729 −0.315 TM ACTATG 1956.85 1038 0.530 −0.634 TN ACCAAC 2378.62 4300 1.808 0.592 TN ACAAAT 1748.34 2194 1.255 0.227 TN ACCAAT 2159.68 2454 1.136 0.128 TN ACAAAC 1925.59 1486 0.772 −0.259 TN ACTAAT 1546.11 1077 0.697 −0.362 TN ACGAAT 709.45 336 0.474 −0.747 TN ACTAAC 1702.85 789 0.463 −0.769 TN ACGAAC 781.37 316 0.404 −0.905 TP ACGCCG 349.03 632 1.811 0.594 TP ACGCCC 963.29 1491 1.548 0.437 TP ACTCCA 1814.66 2359 1.300 0.262 TP ACCCCG 1062.52 1331 1.253 0.225 TP ACTCCT 1880.23 2186 1.163 0.151 TP ACACCA 2052.02 2361 1.151 0.140 TP ACCCCA 2534.80 2784 1.098 0.094 TP ACACCT 2126.17 2104 0.990 −0.010 TP ACCCCT 2626.39 2415 0.920 −0.084 TP ACGCCA 832.67 748 0.898 −0.107 TP ACCCCC 2932.43 2380 0.812 −0.209 TP ACACCC 2373.91 1922 0.810 −0.211 TP ACGCCT 862.76 697 0.808 −0.213 TP ACTCCC 2099.31 1649 0.785 −0.241 TP ACTCCG 760.66 538 0.707 −0.346 TP ACACCG 860.15 534 0.621 −0.477 TQ ACTCAA 1103.35 1368 1.240 0.215 TQ ACCCAG 4303.71 5173 1.202 0.184 TQ ACGCAG 1413.75 1518 1.074 0.071 TQ ACACAA 1247.67 1328 1.064 0.062 TQ ACTCAG 3081.01 2839 0.921 −0.082 TQ ACCCAA 1541.21 1410 0.915 −0.089 TQ ACACAG 3484.02 2765 0.794 −0.231 TQ ACGCAA 506.28 280 0.553 −0.592 TR ACCAGG 1331.08 2049 1.539 0.431 TR ACGCGC 403.79 605 1.498 0.404 TR ACGCGG 441.63 661 1.497 0.403 TR ACTCGA 521.72 717 1.374 0.318 TR ACAAGA 1097.61 1429 1.302 0.264 TR ACCCGC 1229.22 1547 1.259 0.230 TR ACCCGG 1344.40 1668 1.241 0.216 TR ACTCGT 376.76 448 1.189 0.173 TR ACCAGA 1355.85 1599 1.179 0.165 TR ACCCGA 728.77 758 1.040 0.039 TR ACCCGT 526.27 535 1.017 0.016 TR ACAAGG 1077.56 1072 0.995 −0.005 TR ACGAGG 437.25 433 0.990 −0.010 TR ACTCGG 962.45 823 0.855 −0.157 TR ACGCGT 172.88 141 0.816 −0.204 TR ACACGT 426.04 329 0.772 −0.258 TR ACGAGA 445.39 331 0.743 −0.297 TR ACACGA 589.97 432 0.732 −0.312 TR ACACGG 1088.34 756 0.695 −0.364 TR ACTCGC 879.99 607 0.690 −0.371 TR ACTAGA 970.65 624 0.643 −0.442 TR ACGCGA 239.40 150 0.627 −0.468 TR ACACGC 995.10 498 0.500 −0.692 TR ACTAGG 952.91 383 0.402 −0.911 TS ACCAGC 2807.29 4575 1.630 0.488 TS ACCTCG 655.24 1060 1.618 0.481 TS ACGTCG 215.24 348 1.617 0.480 TS ACTTCA 1247.51 1844 1.478 0.391 TS ACTTCT 1543.11 1974 1.279 0.246 TS ACATCA 1410.69 1754 1.243 0.218 TS ACCAGT 1771.14 2194 1.239 0.214 TS ACCTCC 2477.85 3050 1.231 0.208 TS ACCTCA 1742.59 1938 1.112 0.106 TS ACATCT 1744.95 1911 1.095 0.091 TS ACGTCC 813.96 840 1.032 0.031 TS ACCTCT 2155.49 2072 0.961 −0.040 TS ACAAGT 1433.80 1335 0.931 −0.071 TS ACTTCC 1773.89 1524 0.859 −0.152 TS ACGTCA 572.43 450 0.786 −0.241 TS ACATCC 2005.92 1570 0.783 −0.245 TS ACTTCG 469.09 353 0.753 −0.284 TS ACGTCT 708.07 527 0.744 −0.295 TS ACATCG 530.44 361 0.681 −0.385 TS ACTAGT 1267.95 725 0.572 −0.559 TS ACAAGC 2272.61 1275 0.561 −0.578 TS ACGAGT 581.81 297 0.510 −0.672 TS ACGAGC 922.18 469 0.509 −0.676 TS ACTAGC 2009.73 687 0.342 −1.073 TT ACCACG 875.88 1567 1.789 0.582 TT ACCACC 2666.32 4767 1.788 0.581 TT ACCACA 2158.49 2882 1.335 0.289 TT ACCACT 1908.81 2309 1.210 0.190 TT ACAACA 1747.38 1793 1.026 0.026 TT ACAACT 1545.26 1567 1.014 0.014 TT ACGACG 287.72 252 0.876 −0.133 TT ACTACT 1366.51 1065 0.779 −0.249 TT ACTACA 1545.26 1196 0.774 −0.256 TT ACGACC 875.88 575 0.656 −0.421 TT ACGACA 709.06 437 0.616 −0.484 TT ACAACC 2158.49 1310 0.607 −0.499 TT ACGACT 627.04 357 0.569 −0.563 TT ACTACC 1908.81 992 0.520 −0.655 TT ACAACG 709.06 365 0.515 −0.664 TT ACTACG 627.04 283 0.451 −0.796 TV ACTGTA 845.20 1425 1.686 0.522 TV ACTGTT 1301.64 2058 1.581 0.458 TV ACGGTG 1512.80 2306 1.524 0.422 TV ACAGTA 955.76 1371 1.434 0.361 TV ACTGTC 1666.51 2289 1.374 0.317 TV ACAGTT 1471.90 2019 1.372 0.316 TV ACTGTG 3296.87 4505 1.366 0.312 TV ACGGTC 764.70 911 1.191 0.175 TV ACAGTG 3728.11 4108 1.102 0.097 TV ACAGTC 1884.50 1933 1.026 0.025 TV ACGGTA 387.83 286 0.737 −0.305 TV ACGGTT 597.27 415 0.695 −0.364 TV ACCGTG 4605.23 2640 0.573 −0.556 TV ACCGTC 2327.87 1285 0.552 −0.594 TV ACCGTT 1818.19 496 0.273 −1.299 TV ACCGTA 1180.62 298 0.252 −1.377 TW ACGTGG 606.25 837 1.381 0.323 TW ACCTGG 1845.52 2403 1.302 0.264 TW ACATGG 1494.02 1089 0.729 −0.316 TW ACTTGG 1321.21 938 0.710 −0.343 TY ACCTAC 2130.11 3648 1.713 0.538 TY ACCTAT 1730.88 1778 1.027 0.027 TY ACTTAC 1524.94 1383 0.907 −0.098 TY ACGTAC 699.73 621 0.887 −0.119 TY ACATAT 1401.21 1136 0.811 −0.210 TY ACTTAT 1239.13 907 0.732 −0.312 TY ACGTAT 568.59 408 0.718 −0.332 TY ACATAC 1724.41 1138 0.660 −0.416 VA GTGGCC 6082.92 9316 1.532 0.426 VA GTAGCA 897.78 1347 1.500 0.406 VA GTTGCT 1579.41 2217 1.404 0.339 VA GTAGCT 1025.57 1407 1.372 0.316 VA GTGGCT 4000.44 5252 1.313 0.272 VA GTGGCG 1644.71 2099 1.276 0.244 VA GTTGCA 1382.62 1728 1.250 0.223 VA GTGGCA 3501.98 3859 1.102 0.097 VA GTAGCC 1559.44 1363 0.874 −0.135 VA GTTGCC 2401.60 1808 0.753 −0.284 VA GTAGCG 421.64 216 0.512 −0.669 VA GTTGCG 649.35 234 0.360 −1.021 VA GTCGCG 831.37 284 0.342 −1.074 VA GTCGCC 3074.82 992 0.323 −1.131 VA GTCGCT 2022.16 406 0.201 −1.606 VA GTCGCA 1770.19 318 0.180 −1.717 VC GTCTGC 1410.66 2160 1.531 0.426 VC GTCTGT 1188.18 1572 1.323 0.280 VC GTTTGT 928.03 942 1.015 0.015 VC GTATGT 602.60 594 0.986 −0.014 VC GTGTGC 2790.71 2583 0.926 −0.077 VC GTGTGT 2350.57 1996 0.849 −0.164 VC GTTTGC 1101.80 830 0.753 −0.283 VC GTATGC 715.44 411 0.574 −0.554 VD GTAGAT 1225.65 1924 1.570 0.451 VD GTGGAC 5400.58 7734 1.432 0.359 VD GTTGAT 1887.55 2389 1.266 0.236 VD GTGGAT 4780.91 5727 1.198 0.181 VD GTAGAC 1384.52 1346 0.972 −0.028 VD GTTGAC 2132.21 1791 0.840 −0.174 VD GTCGAC 2729.91 602 0.221 −1.512 VD GTCGAT 2416.67 445 0.184 −1.692 VE GTAGAA 1456.83 2855 1.960 0.673 VE GTGGAG 7599.48 11579 1.524 0.421 VE GTTGAA 2243.56 2905 1.295 0.258 VE GTGGAA 5682.64 6229 1.096 0.092 VE GTAGAG 1948.24 2002 1.028 0.027 VE GTTGAG 3000.36 1987 0.662 −0.412 VE GTCGAG 3841.42 721 0.188 −1.673 VE GTCGAA 2872.48 367 0.128 −2.058 VF GTCTTC 2309.08 4216 1.826 0.602 VF GTATTT 1023.16 1512 1.478 0.391 VF GTCTTT 2017.40 2238 1.109 0.104 VF GTTTTT 1575.70 1706 1.083 0.079 VF GTTTTC 1803.52 1604 0.889 −0.117 VF GTGTTT 3991.02 3257 0.816 −0.203 VF GTGTTC 4568.05 3205 0.702 −0.354 VF GTATTC 1171.09 721 0.616 −0.485 VG GTTGGT 779.74 1617 2.074 0.729 VG GTTGGA 1204.37 2315 1.922 0.653 VG GTGGGC 4136.07 5977 1.445 0.368 VG GTAGGA 782.04 1089 1.393 0.331 VG GTTGGG 1175.77 1510 1.284 0.250 VG GTTGGC 1632.96 1794 1.099 0.094 VG GTAGGT 506.31 554 1.094 0.090 VG GTGGGG 2978.07 3255 1.093 0.089 VG GTGGGT 1974.96 2009 1.017 0.017 VG GTAGGG 763.47 683 0.895 −0.111 VG GTGGGA 3050.51 2599 0.852 −0.160 VG GTAGGC 1060.34 676 0.638 −0.450 VG GTCGGG 1505.36 734 0.488 −0.718 VG GTCGGC 2090.72 734 0.351 −1.047 VG GTCGGT 998.31 292 0.292 −1.229 VG GTCGGA 1541.98 343 0.222 −1.503 VH GTTCAT 911.79 1418 1.555 0.442 VH GTACAT 592.06 773 1.306 0.267 VH GTCCAC 1609.82 2085 1.295 0.259 VH GTCCAT 1167.39 1313 1.125 0.118 VH GTTCAC 1257.35 1319 1.049 0.048 VH GTGCAC 3184.70 2856 0.897 −0.109 VH GTACAC 816.44 613 0.751 −0.287 VH GTGCAT 2309.44 1472 0.637 −0.450 VI GTCATC 2367.78 5207 2.199 0.788 VI GTCATT 1872.41 2827 1.510 0.412 VI GTAATA 436.74 614 1.406 0.341 VI GTAATT 949.63 1074 1.131 0.123 VI GTTATT 1462.46 1595 1.091 0.087 VI GTCATA 861.15 904 1.050 0.049 VI GTTATA 672.60 702 1.044 0.043 VI GTGATT 3704.20 2742 0.740 −0.301 VI GTGATC 4684.19 3353 0.716 −0.334 VI GTGATA 1703.61 1117 0.656 −0.422 VI GTTATC 1849.37 1053 0.569 −0.563 VI GTAATC 1200.86 577 0.480 −0.733 VK GTAAAA 1288.46 1945 1.510 0.412 VK GTCAAG 3290.24 3982 1.210 0.191 VK GTGAAG 6509.08 7513 1.154 0.143 VK GTAAAG 1668.70 1704 1.021 0.021 VK GTCAAA 2540.51 2376 0.935 −0.067 VK GTTAAA 1984.27 1777 0.896 −0.110 VK GTGAAA 5025.89 4409 0.877 −0.131 VK GTTAAG 2569.85 1171 0.456 −0.786 VL GTTTTA 668.83 1311 1.960 0.673 VL GTTCTT 1146.70 1859 1.621 0.483 VL GTTTTG 1123.58 1737 1.546 0.436 VL GTATTA 434.30 646 1.487 0.397 VL GTCCTC 2129.16 3019 1.418 0.349 VL GTTCTA 618.41 832 1.345 0.297 VL GTCCTG 4424.65 5574 1.260 0.231 VL GTCCTT 1468.14 1722 1.173 0.159 VL GTGCTG 8753.31 10107 1.155 0.144 VL GTCTTG 1438.54 1628 1.132 0.124 VL GTACTA 401.55 447 1.113 0.107 VL GTCCTA 791.76 874 1.104 0.099 VL GTCTTA 856.32 863 1.008 0.008 VL GTATTG 729.58 711 0.975 −0.026 VL GTACTT 744.59 693 0.931 −0.072 VL GTTCTC 1662.99 1501 0.903 −0.102 VL GTGCTC 4212.12 3765 0.894 −0.112 VL GTGCTA 1566.34 1286 0.821 −0.197 VL GTTCTG 3455.90 2350 0.680 −0.386 VL GTGTTG 2845.87 1910 0.671 −0.399 VL GTGCTT 2904.43 1933 0.666 −0.407 VL GTGTTA 1694.06 965 0.570 −0.563 VL GTACTC 1079.84 541 0.501 −0.691 VL GTACTG 2244.04 1121 0.500 −0.694 VM GTCATG 2149.52 3308 1.539 0.431 VM GTGATG 4252.41 3872 0.911 −0.094 VM GTAATG 1090.17 935 0.858 −0.154 VM GTTATG 1678.90 1056 0.629 −0.464 VN GTCAAC 2052.00 3311 1.614 0.478 VN GTAAAT 944.92 1518 1.606 0.474 VN GTCAAT 1863.13 2155 1.157 0.146 VN GTTAAT 1455.20 1325 0.911 −0.094 VN GTGAAC 4059.49 3551 0.875 −0.134 VN GTGAAT 3685.83 3110 0.844 −0.170 VN GTAAAC 1040.71 854 0.821 −0.198 VN GTTAAC 1602.73 880 0.549 −0.600 VP GTTCCT 1434.04 2257 1.574 0.454 VP GTTCCA 1384.03 1911 1.381 0.323 VP GTGCCC 4055.45 4998 1.232 0.209 VP GTACCT 931.17 1048 1.125 0.118 VP GTCCCC 2049.96 2260 1.102 0.098 VP GTCCCT 1836.02 2014 1.097 0.093 VP GTACCA 898.70 963 1.072 0.069 VP GTCCCG 742.77 786 1.058 0.057 VP GTTCCC 1601.13 1506 0.941 −0.061 VP GTCCCA 1772.00 1596 0.901 −0.105 VP GTGCCT 3632.21 3062 0.843 −0.171 VP GTGCCG 1469.43 1228 0.836 −0.179 VP GTACCC 1039.67 809 0.778 −0.251 VP GTGCCA 3505.55 2431 0.693 −0.366 VP GTTCCG 580.15 279 0.481 −0.732 VP GTACCG 376.71 161 0.427 −0.850 VQ GTACAA 633.37 1049 1.656 0.505 VQ GTTCAA 975.42 1485 1.522 0.420 VQ GTCCAG 3487.32 3907 1.120 0.114 VQ GTACAG 1768.65 1752 0.991 −0.009 VQ GTTCAG 2723.79 2689 0.987 −0.013 VQ GTGCAG 6898.98 6734 0.976 −0.024 VQ GTCCAA 1248.85 1067 0.854 −0.157 VQ GTGCAA 2470.60 1524 0.617 −0.483 VR GTTCGA 463.33 867 1.871 0.627 VR GTTCGT 334.59 580 1.733 0.550 VR GTCCGA 593.21 805 1.357 0.305 VR GTCCGC 1000.57 1332 1.331 0.286 VR GTGCGC 1979.43 2543 1.285 0.251 VR GTCCGT 428.38 549 1.282 0.248 VR GTCCGG 1094.32 1346 1.230 0.207 VR GTACGA 300.86 361 1.200 0.182 VR GTAAGA 559.73 660 1.179 0.165 VR GTGCGG 2164.91 2552 1.179 0.164 VR GTCAGA 1103.65 1291 1.170 0.157 VR GTACGT 217.26 253 1.165 0.152 VR GTCAGG 1083.48 1238 1.143 0.133 VR GTGAGG 2143.46 1986 0.927 −0.076 VR GTGCGT 847.46 761 0.898 −0.108 VR GTAAGG 549.51 444 0.808 −0.213 VR GTTCGG 854.73 650 0.760 −0.274 VR GTGCGA 1173.55 826 0.704 −0.351 VR GTTCGC 781.50 545 0.697 −0.360 VR GTGAGA 2183.35 1511 0.692 −0.368 VR GTACGG 555.00 377 0.679 −0.387 VR GTTAGA 862.01 556 0.645 −0.438 VR GTACGC 507.46 286 0.564 −0.573 VR GTTAGG 846.26 309 0.365 −1.007 VS GTTTCT 1206.81 2161 1.791 0.583 VS GTCTCC 1776.18 2936 1.653 0.503 VS GTCAGC 2012.32 3223 1.602 0.471 VS GTTTCA 975.63 1465 1.502 0.407 VS GTCAGT 1269.59 1841 1.450 0.372 VS GTATCT 783.62 1093 1.395 0.333 VS GTATCA 633.51 806 1.272 0.241 VS GTCTCT 1545.10 1847 1.195 0.178 VS GTTTCC 1387.29 1604 1.156 0.145 VS GTCTCG 469.69 542 1.154 0.143 VS GTCTCA 1249.12 1333 1.067 0.065 VS GTGTCC 3513.81 3722 1.059 0.058 VS GTGTCG 929.19 860 0.926 −0.077 VS GTGTCT 3056.67 2784 0.911 −0.093 VS GTATCC 900.82 763 0.847 −0.166 VS GTAAGT 643.89 499 0.775 −0.255 VS GTGAGC 3980.98 2901 0.729 −0.316 VS GTGTCA 2471.14 1710 0.692 −0.368 VS GTTAGT 991.62 640 0.645 −0.438 VS GTATCG 238.21 138 0.579 −0.546 VS GTTTCG 366.85 202 0.551 −0.597 VS GTGAGT 2511.63 1371 0.546 −0.605 VS GTAAGC 1020.58 514 0.504 −0.686 VS GTTAGC 1571.73 551 0.351 −1.048 VT GTCACC 2294.69 4477 1.951 0.668 VT GTCACT 1642.76 2452 1.493 0.401 VT GTCACG 753.80 997 1.323 0.280 VT GTAACT 833.15 1046 1.255 0.228 VT GTCACA 1857.64 2207 1.188 0.172 VT GTAACA 942.13 1096 1.163 0.151 VT GTTACT 1283.09 1208 0.941 −0.060 VT GTGACC 4539.59 4223 0.930 −0.072 VT GTGACG 1491.24 1318 0.884 −0.123 VT GTGACT 3249.88 2758 0.849 −0.164 VT GTGACA 3674.98 2947 0.802 −0.221 VT GTTACA 1450.92 1111 0.766 −0.267 VT GTAACC 1163.79 758 0.651 −0.429 VT GTTACC 1792.28 969 0.541 −0.615 VT GTAACG 382.30 191 0.500 −0.694 VT GTTACG 588.76 183 0.311 −1.169 VV GTTGTA 655.54 1109 1.692 0.526 VV GTTGTT 1009.55 1701 1.685 0.522 VV GTAGTA 425.66 698 1.640 0.495 VV GTGGTG 6476.64 9025 1.393 0.332 VV GTGGTC 3273.84 4256 1.300 0.262 VV GTAGTT 655.54 800 1.220 0.199 VV GTTGTC 1292.55 1561 1.208 0.189 VV GTGGTA 1660.38 1777 1.070 0.068 VV GTGGTT 2557.05 2613 1.022 0.022 VV GTTGTG 2557.05 2261 0.884 −0.123 VV GTAGTG 1660.38 1161 0.699 −0.358 VV GTAGTC 839.30 553 0.659 −0.417 VV GTCGTC 1654.87 858 0.518 −0.657 VV GTCGTG 3273.84 1250 0.382 −0.963 VV GTCGTA 839.30 213 0.254 −1.371 VV GTCGTT 1292.55 288 0.223 −1.501 VW GTCTGG 1316.29 1763 1.339 0.292 VW GTGTGG 2604.03 2451 0.941 −0.061 VW GTATGG 667.58 578 0.866 −0.144 VW GTTTGG 1028.10 824 0.801 −0.221 VY GTCTAC 1602.79 2490 1.554 0.441 VY GTTTAT 1017.23 1438 1.414 0.346 VY GTATAT 660.53 875 1.325 0.281 VY GTCTAT 1302.39 1544 1.186 0.170 VY GTGTAC 3170.80 2654 0.837 −0.178 VY GTTTAC 1251.87 1008 0.805 −0.217 VY GTATAC 812.88 582 0.716 −0.334 VY GTGTAT 2576.51 1804 0.700 −0.356 WA TGGGCA 1469.77 1535 1.044 0.043 WA TGGGCG 690.28 695 1.007 0.007 WA TGGGCT 1678.97 1664 0.991 −0.009 WA TGGGCC 2552.98 2498 0.978 −0.022 WC TGGTGC 1057.38 1066 1.008 0.008 WC TGGTGT 890.62 882 0.990 −0.010 WD TGGGAC 2699.37 2807 1.040 0.039 WD TGGGAT 2389.63 2282 0.955 −0.046 WE TGGGAG 3580.00 3650 1.020 0.019 WE TGGGAA 2677.00 2607 0.974 −0.026 WF TGGTTT 1639.95 1735 1.058 0.056 WF TGGTTC 1877.05 1782 0.949 −0.052 WG TGGGGT 955.95 1064 1.113 0.107 WG TGGGGC 2002.00 2179 1.088 0.085 WG TGGGGA 1476.56 1454 0.985 −0.015 WG TGGGGG 1441.49 1179 0.818 −0.201 WH TGGCAT 971.42 1000 1.029 0.029 WH TGGCAC 1339.58 1311 0.979 −0.022 WI TGGATT 1537.91 1627 1.058 0.056 WI TGGATA 707.30 714 1.009 0.009 WI TGGATC 1944.78 1849 0.951 −0.051 WK TGGAAG 3491.83 3645 1.044 0.043 WK TGGAAA 2696.17 2543 0.943 −0.058 WL TGGCTA 683.88 798 1.167 0.154 WL TGGCTG 3821.78 4228 1.106 0.101 WL TGGCTT 1268.11 1334 1.052 0.051 WL TGGCTC 1839.05 1879 1.022 0.021 WL TGGTTG 1242.54 855 0.688 −0.374 WL TGGTTA 739.64 501 0.677 −0.390 WM TGGATG 2335.00 2335 1.000 0.000 WN TGGAAT 1978.70 2005 1.013 0.013 WN TGGAAC 2179.30 2153 0.988 −0.012 WP TGGCCC 1302.21 1381 1.061 0.059 WP TGGCCG 471.84 486 1.030 0.030 WP TGGCCA 1125.64 1123 0.998 −0.002 WP TGGCCT 1166.31 1076 0.923 −0.081 WQ TGGCAG 2983.56 2997 1.005 0.004 WQ TGGCAA 1068.44 1055 0.987 −0.013 WR TGGAGG 1198.99 1665 1.389 0.328 WR TGGAGA 1221.30 1472 1.205 0.187 WR TGGCGG 1210.98 979 0.808 −0.213 WR TGGCGC 1107.23 895 0.808 −0.213 WR TGGCGT 474.05 377 0.795 −0.229 WR TGGCGA 656.45 481 0.733 −0.311 WS TGGAGT 1031.75 1239 1.201 0.183 WS TGGAGC 1635.35 1956 1.196 0.179 WS TGGTCA 1015.12 898 0.885 −0.123 WS TGGTCC 1443.44 1271 0.881 −0.127 WS TGGTCT 1255.65 1076 0.857 −0.154 WS TGGTCG 381.70 323 0.846 −0.167 WT TGGACG 598.07 674 1.127 0.120 WT TGGACA 1473.88 1559 1.058 0.056 WT TGGACT 1303.39 1240 0.951 −0.050 WT TGGACC 1820.65 1723 0.946 −0.055 WV TGGGTC 1318.64 1378 1.045 0.044 WV TGGGTG 2608.66 2633 1.009 0.009 WV TGGGTA 668.77 665 0.994 −0.006 WV TGGGTT 1029.93 950 0.922 −0.081 WW TGGTGG 1559.00 1559 1.000 0.000 WY TGGTAC 1444.91 1520 1.052 0.051 WY TGGTAT 1174.09 1099 0.936 −0.066 YA TATGCA 1120.39 2249 2.007 0.697 YA TATGCT 1279.86 2296 1.794 0.584 YA TATGCC 1946.11 2862 1.471 0.386 YA TACGCG 647.56 622 0.961 −0.040 YA TATGCG 526.19 482 0.916 −0.088 YA TACGCC 2395.00 1402 0.585 −0.535 YA TACGCA 1378.81 512 0.371 −0.991 YA TACGCT 1575.07 444 0.282 −1.266 YC TACTGC 1588.07 2411 1.518 0.418 YC TACTGT 1337.61 1587 1.186 0.171 YC TATTGT 1086.90 659 0.606 −0.500 YC TATTGC 1290.42 646 0.501 −0.692 YD TATGAT 2091.17 3707 1.773 0.572 YD TATGAC 2362.22 3731 1.579 0.457 YD TACGAC 2907.08 1653 0.569 −0.565 YD TACGAT 2573.52 843 0.328 −1.116 YE TATGAA 2515.85 5225 2.077 0.731 YE TATGAG 3364.48 4722 1.403 0.339 YE TACGAG 4140.53 2309 0.558 −0.584 YE TACGAA 3096.14 861 0.278 −1.280 YF TACTTC 2766.63 3380 1.222 0.200 YF TATTTT 1964.12 2124 1.081 0.078 YF TACTTT 2417.16 2201 0.911 −0.094 YF TATTTC 2248.09 1691 0.752 −0.285 YG TATGGA 1472.35 2874 1.952 0.669 YG TATGGT 953.23 1665 1.747 0.558 YG TATGGG 1437.38 2129 1.481 0.393 YG TATGGC 1996.30 2749 1.377 0.320 YG TACGGG 1768.93 1088 0.615 −0.486 YG TACGGC 2456.76 1484 0.604 −0.504 YG TACGGT 1173.10 448 0.382 −0.963 YG TACGGA 1811.96 633 0.349 −1.052 YH TACCAC 1862.81 2378 1.277 0.244 YH TACCAT 1350.85 1420 1.051 0.050 YH TATCAT 1097.67 1021 0.930 −0.072 YH TATCAC 1513.67 1006 0.665 −0.409 YI TACATC 2684.66 3935 1.466 0.382 YI TACATT 2122.99 2162 1.018 0.018 YI TATATT 1725.09 1554 0.901 −0.104 YI TACATA 976.39 846 0.866 −0.143 YI TATATA 793.39 648 0.817 −0.202 YI TATATC 2181.48 1339 0.614 −0.488 YK TACAAG 3508.58 4372 1.246 0.220 YK TACAAA 2709.10 2847 1.051 0.050 YK TATAAA 2201.34 2262 1.028 0.027 YK TATAAG 2850.98 1789 0.628 −0.466 YL TACCTG 4522.42 6324 1.398 0.335 YL TATTTA 711.20 966 1.358 0.306 YL TACCTC 2176.20 2598 1.194 0.177 YL TACTTG 1470.33 1701 1.157 0.146 YL TATTTG 1194.75 1358 1.137 0.128 YL TACCTA 809.25 876 1.082 0.079 YL TACCTT 1500.58 1449 0.966 −0.035 YL TATCTT 1219.33 1166 0.956 −0.045 YL TACTTA 875.24 763 0.872 −0.137 YL TATCTA 657.58 541 0.823 −0.195 YL TATCTC 1768.32 1087 0.615 −0.487 YL TATCTG 3674.80 1751 0.476 −0.741 YM TACATG 2325.97 3055 1.313 0.273 YM TATATG 1890.03 1161 0.614 −0.487 YN TACAAC 2442.24 3341 1.368 0.313 YN TACAAT 2217.44 2200 0.992 −0.008 YN TATAAT 1801.83 1629 0.904 −0.101 YN TATAAC 1984.50 1276 0.643 −0.442 YP TACCCG 668.65 1004 1.502 0.406 YP TACCCA 1595.15 1925 1.207 0.188 YP TATCCA 1296.18 1438 1.109 0.104 YP TACCCC 1845.38 1961 1.063 0.061 YP TATCCT 1343.02 1379 1.027 0.026 YP TACCCT 1652.79 1558 0.943 −0.059 YP TATCCC 1499.51 937 0.625 −0.470 YP TATCCG 543.32 242 0.445 −0.809 YQ TACCAG 3987.12 5013 1.257 0.229 YQ TATCAA 1160.22 1179 1.016 0.016 YQ TACCAA 1427.83 1397 0.978 −0.022 YQ TATCAG 3239.83 2226 0.687 −0.375 YR TACCGC 1307.70 2153 1.646 0.499 YR TACCGA 775.30 990 1.277 0.244 YR TACAGA 1442.41 1834 1.271 0.240 YR TACCGG 1430.23 1796 1.256 0.228 YR TACAGG 1416.06 1671 1.180 0.166 YR TACCGT 559.87 642 1.147 0.137 YR TATCGA 629.99 570 0.905 −0.100 YR TATCGT 454.94 383 0.842 −0.172 YR TATAGA 1172.07 827 0.706 −0.349 YR TATCGG 1162.17 629 0.541 −0.614 YR TATAGG 1150.66 560 0.487 −0.720 YR TATCGC 1062.60 509 0.479 −0.736 YS TACAGC 2204.13 3590 1.629 0.488 YS TACTCG 514.46 783 1.522 0.420 YS TACAGT 1390.60 1887 1.357 0.305 YS TATTCA 1111.75 1210 1.088 0.085 YS TACTCC 1945.47 2088 1.073 0.071 YS TATTCT 1375.18 1466 1.066 0.064 YS TACTCA 1368.18 1188 0.868 −0.141 YS TATTCC 1580.84 1306 0.826 −0.191 YS TACTCT 1692.37 1173 0.693 −0.367 YS TATAGT 1129.96 728 0.644 −0.440 YS TATTCG 418.04 229 0.548 −0.602 YS TATAGC 1791.02 874 0.488 −0.717 YT TACACG 697.26 1311 1.880 0.631 YT TACACC 2122.58 2696 1.270 0.239 YT TACACA 1718.31 2158 1.256 0.228 YT TACACT 1519.54 1409 0.927 −0.076 YT TATACT 1234.74 1049 0.850 −0.163 YT TATACA 1396.25 1049 0.751 −0.286 YT TATACC 1724.75 1063 0.616 −0.484 YT TATACG 566.57 245 0.432 −0.838 YV TATGTT 986.79 1723 1.746 0.557 YV TATGTA 640.76 1113 1.737 0.552 YV TATGTC 1263.40 1862 1.474 0.388 YV TATGTG 2499.39 3382 1.353 0.302 YV TACGTG 3075.90 2279 0.741 −0.300 YV TACGTC 1554.82 991 0.637 −0.450 YV TACGTA 788.55 284 0.360 −1.021 YV TACGTT 1214.40 390 0.321 −1.136 YW TACTGG 1609.87 2212 1.374 0.318 YW TATTGG 1308.13 706 0.540 −0.617 YY TACTAC 2256.03 2854 1.265 0.235 YY TATTAT 1489.60 1459 0.979 −0.021 YY TACTAT 1833.19 1760 0.960 −0.041 YY TATTAC 1833.19 1339 0.730 −0.314 

1-11. (canceled)
 12. A modified influenza virus genome having a recoded hemagglutinin (HA) protein-encoding sequence and a recoded neuraminidase (NA) protein-encoding sequence, wherein the other influenza protein-encoding sequences are not recoded.
 13. The modified influenza virus genome of claim 12, wherein the HA protein-encoding sequence, the NA protein-encoding sequence, or both are recoded by one or more of lowering the codon pair bias of the protein-encoding sequence; lowering the codon bias of the protein-encoding sequence; and modifying the CG and/or TA dinucleotide content of the protein-encoding sequence.
 14. The modified influenza virus genome of claim 12, wherein the HA protein-encoding sequence, the NA protein-encoding sequence, or both are recoded by lowering the codon pair bias of the protein-encoding sequence.
 15. The modified influenza virus genome of claim 14, wherein reducing the codon-pair bias comprises identifying a codon pair in the parent protein-encoding sequence having a codon-pair score that can be reduced, and reducing the codon-pair bias by substituting the codon pair with a codon pair that encodes the same codon and has a lower codon-pair score.
 16. The modified influenza virus genome of claim 14, wherein reducing the codon-pair bias comprises rearranging the codons of a parent protein-encoding sequence, wherein the rearranged sequence encodes the same protein as the parent protein-encoding sequence.
 17. The modified influenza virus genome of claim 15, wherein each of the recoded HA protein-encoding sequence and the recoded NA protein-encoding sequence have a codon pair bias less than −0.1, or less than −0.2, or less than −0.3, or less than −0.4.
 18. The modified influenza virus genome of claim 12, wherein the HA protein-encoding sequence, the NA protein-encoding sequence, or both are recoded by replacing one or more codons with synonymous codons that are less frequent in the viral host.
 19. The modified influenza virus genome of claim 12, the HA protein-encoding sequence, the NA protein-encoding sequence, or both are recoded by modifying the CG dinucleotide content, the TA dinucleotide content, or both.
 20. A modified influenza virus comprising the modified influenza virus genome of claim
 12. 21. The modified influenza virus of claim 20 wherein the expression of the recoded hemagglutinin-encoding nucleotide sequence and expression of the recoded neuraminidase-encoding nucleotide sequence is reduced compared to the parent virus.
 22. A vaccine composition for inducing a protective immune response in a subject, which comprises the modified influenza virus of claim
 20. 23. The vaccine composition of claim 22, further comprising at least one adjuvant.
 24. The vaccine composition of claim 22, wherein the protective immune response is cross-protective against a heterologous influenza virus. 